WO2003035833A2 - Modificateurs de la voie de passage de p53 et leurs procedes d'utilisation - Google Patents

Modificateurs de la voie de passage de p53 et leurs procedes d'utilisation Download PDF

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WO2003035833A2
WO2003035833A2 PCT/US2002/033542 US0233542W WO03035833A2 WO 2003035833 A2 WO2003035833 A2 WO 2003035833A2 US 0233542 W US0233542 W US 0233542W WO 03035833 A2 WO03035833 A2 WO 03035833A2
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agent
assay
cell
candidate
pathway
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WO2003035833A3 (fr
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Marcia Belvin
Helen Francis-Lang
Gregory D. Plowman
Roel P. Funke
Danxi Li
Lori Friedman
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Exelixis, Inc.
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • C—CHEMISTRY; METALLURGY
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/34—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase
    • C12Q1/42—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase involving phosphatase
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/5011—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics for testing antineoplastic activity
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/5308—Immunoassay; Biospecific binding assay; Materials therefor for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • G01N33/57415—Specifically defined cancers of breast
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57484—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6872—Intracellular protein regulatory factors and their receptors, e.g. including ion channels
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
    • G01N2333/46—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans from vertebrates
    • G01N2333/47—Assays involving proteins of known structure or function as defined in the subgroups
    • G01N2333/4701—Details
    • G01N2333/4739—Cyclin; Prad 1
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value
    • G01N2500/10—Screening for compounds of potential therapeutic value involving cells
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2510/00—Detection of programmed cell death, i.e. apoptosis

Definitions

  • the p53 gene is mutated in over 50 different types of human cancers, including familial and spontaneous cancers, and is believed to be the most commonly mutated gene in human cancer (Zambetti and Levine, FASEB (1993) 7:855-865; Hollstein, et al, Nucleic Acids Res. (1994) 22:3551-3555). Greater than 90% of mutations in the p53 gene are missense mutations that alter a single amino acid that inactivates p53 function.
  • the human p53 protein normally functions as a central integrator of signals including DNA damage, hypoxia, nucleotide deprivation, and oncogene activation (Prives, Cell (1998) 95:5-8). In response to these signals, p53 protein levels are greatly increased with the result that the accumulated p53 activates cell cycle arrest or apoptosis depending on the nature and strength of these signals. Indeed, multiple lines of experimental evidence have pointed to a key role for p53 as a tumor suppressor (Levine, Cell (1997) 88:323-331). For example, homozygous p53 "knockout" mice are developmentally normal but exhibit nearly 100% incidence of neoplasia in the first year of life (Donehower et al., Nature (1992) 356:215-221).
  • p53 function is its activity as a gene-specific transcriptional activator.
  • genes with known p53-response elements are several with well-characterized roles in either regulation of the cell cycle or apoptosis, including GADD45, p21/Waf 1/Cipl, cyclin G, Bax, IGF- BP3, and MDM2 (Levine, Cell (1997) 88:323-331).
  • LRRs Leucine-rich repeats
  • LRR-containing proteins include the binding of enzymes (Tan, F. et al. (1990) J Biol Chem; 265(1): 13-9) and vascular repair (Hickey, M. (1989) Proc Natl Acad Sci U S A; 86(17): 6773-7).
  • LRRs form elongated non-globular structures and are often flanked by cysteine rich domains.
  • LRRN1 is a protein containing nine LRRs, leucine rich repeat C- terminal and N- terminal cysteine rich domains, and an immunoglobulin (lg) domain. It shares sequence similarity with D2S448, a melanoma associated gene (Nagase, T. et al. (2000) DNA Res; 7(2): 143-50).
  • IGFl insulin-like growth factors
  • IGF2 insulin-like growth factors
  • IGF2 insulin-like growth factors
  • IGF2 insulin-like growth factors
  • IGF2 insulin-like growth factors
  • IGF2 insulin-like growth factors
  • IGF2 insulin-like growth factors
  • IGF2 insulin-like growth factors
  • IGFs In juvenile and adult mammals, however, 80% to 85% of serum IGFs are found in a ternary complex composed of 1 molecule each of IGF, IGFBP3, and a protein that is found only in serum, the acid-labile subunit (ALS). ALS retains the IGFBP3/IGF complexes in the vascular compartment and extends the half life of IGFs in the circulation. Synthesis of ALS occurs mainly in liver after birth and is stimulated by growth hormone. Insulin-like growth factor binding protein acid-labile subunit (IGFALS) mediates the formation of IGFl and IGFBP3 complex (Leong, S. R., et al (1992) Mol Endocrinol 6:870-6).
  • IGFALS Insulin-like growth factor binding protein acid-labile subunit
  • IGFALS is required for postnatal accumulation of IGFl and IGFBP3 but, consistent with findings supporting a predominant role for locally produced IGFl, is not critical for growth. IGFALS is necessary for blood sugar regulation, and shows deficiency in non islet cell tumor hypoglycemia syndrome and in liver cirrhosis (Ottesen, L. H., et al (2001) Liver 21: 350-6; Baxter, R. C. (1996) Horm Res 46, 195-201).
  • the DNA ligase activity in most proliferating mammalian cells is due to the high molecular weight enzyme designated DNA ligase I (LIG1). It acts as a DNA replication and repair enzyme (Lindahl, T.; Barnes, D. (1992) Annu. Rev.
  • NAG14 is a protein containing eight LRRs, leucine rich repeat C-terminal and N- terminal cysteine rich domains, and an immunoglobulin (lg) domain. It is similar to chondroadherin (Shen, Z. et al. (1998) Biochem J; 330 ( Pt l):549-57).
  • KIAA1580 is a protein containing an immunoglobulin (lg) domain, a leucine rich repeat N-terminal and C-terminal cysteine rich domain and nine LRRs. It is similar to glycoprotein V (Kitaguchi, T. et al. (1997) Thromb Res; 87(2):235-44).
  • DKFZp76 is a protein containing three LRRs, a leucine rich repeat C-terminal cysteine rich domain and an immunoglobulin (lg) domain. It has a region of low homology to a region of melanoma associated gene D2S448.
  • the FLRT family of proteins structurally resembles small leucine-rich proteoglycans found in the extracellular matrix (ECM).
  • ECM extracellular matrix
  • the ECM is composed of collagens, proteoglycans, and noncollagenous glycoproteins, which provide cells and tissues with a mechanical scaffold for adhesion, migration, and signal transduction. These functions are varied and complex and depend on interactions between ECM components and cellular receptors, such as integrins and proteoglycans, which are located at the cell surface (Lacy, S. et al. (1999) Genomics 62: 417-426).
  • FLRTI Fibronectin leucine rich transmembrane protein 1
  • FLRTI Fibronectin leucine rich transmembrane protein 1
  • FLRT2 (KIAA0405) is a protein with eighteen LRRs, two leucine rich repeat C- terminal and two leucine rich repeat N-terminal cysteine rich domains and two fibronectin type HI domains. It is similar to mouse fibromodulin (Ishikawa et al. (1997) DNA Res. 4: 307-313). FLRT2 is expressed in pancreas, skeletal muscle, brain, and heart. FLRT2 is also thought to be involved in cell adhesion and/or receptor signaling (Lacy, S. et al. (1999) supra). Fibronectin leucine rich transmembrane protein 3 (FLRT3) is also a member of the FLRT3.
  • FLRT family which has a putative type I membrane protein with ten LRRs flanked by cysteine-rich regions. It may function as a receptor involved in cell-cell contact and cell adhesion (Lacy, S. et al. (1999) supra).
  • FLRT3 is expressed in kidney, skeletal muscle, lung, and brain, and at lower levels in pancreas, liver, placenta, and heart.
  • the ability to manipulate the genomes of model organisms such as Drosophila provides a powerful means to analyze biochemical processes that, due to significant evolutionary conservation, have direct relevance to more complex vertebrate organisms.
  • a genetic screen can be carried out in an invertebrate model organism having underexpression (e.g. knockout) or overexpression of a gene (referred to as a "genetic entry point") that yields a visible phenotype. Additional genes are mutated in a random or targeted manner.
  • a gene mutation changes the original phenotype caused by the mutation in the genetic entry point, the gene is identified as a "modifier" involved in the same or overlapping pathway as the genetic entry point.
  • modifier genes can be identified that may be attractive candidate targets for novel therapeutics.
  • HM-modulating agents that are candidate therapeutic agents that can be used in the treatment of disorders associated with defective or impaired p53 function and/or HM function.
  • Preferred HM-modulating agents specifically bind to HM polypeptides and restore p53 function.
  • Other preferred HM-modulating agents are nucleic acid modulators such as antisense oligomers and RNAi that repress HM gene expression or product activity by, for example, binding to and inhibiting the respective nucleic acid (i.e. DNA or mRNA).
  • HM modulating agents may be evaluated by any convenient in vitro or in vivo assay for molecular interaction with an HM polypeptide or nucleic acid.
  • candidate HM modulating agents are tested with an assay system comprising an HM polypeptide or nucleic acid.
  • Agents that produce a change in the activity of the assay system relative to controls are identified as candidate p53 modulating agents.
  • the assay system may be cell-based or cell-free.
  • HM-modulating agents include HM related proteins (e.g. dominant negative mutants, and biotherapeutics); HM-specific antibodies; HM-specific antisense oligomers and other nucleic acid modulators; and chemical agents that specifically bind to or interact with HM or compete with HM binding partner (e.g.
  • a small molecule modulator is identified using a binding assay.
  • the screening assay system is selected from an apoptosis assay, a cell proliferation assay, an angiogenesis assay, and a hypoxic induction assay.
  • candidate p53 pathway modulating agents are further tested using a second assay system that detects changes in the p53 pathway, such as angiogenic, apoptotic, or cell proliferation changes produced by the originally identified candidate agent or an agent derived from the original agent.
  • the second assay system may use cultured cells or non-human animals.
  • the secondary assay system uses non-human animals, including animals predetermined to have a disease or disorder implicating the p53 pathway, such as an angiogenic, apoptotic, or cell proliferation disorder (e.g. cancer).
  • the invention further provides methods for modulating the HM function and/or the p53 pathway in a mammalian cell by contacting the mammalian cell with an agent that specifically binds an HM polypeptide or nucleic acid.
  • the agent may be a small molecule modulator, a nucleic acid modulator, or an antibody and may be administered to a mammalian animal predetermined to have a pathology associated the p53 pathway.
  • HM Human modifiers
  • HM- modulating agents that act by inhibiting or enhancing HM expression, directly or indirectly, for example, by affecting an HM function such as binding activity, can be identified using methods provided herein. HM modulating agents are useful in diagnosis, therapy and pharmaceutical development.
  • HM nucleic acids and polypeptides that can be used in the invention are disclosed in Genbank (referenced by Genbank identifier (GI) or RefSeq number), and shown in Table 1. SEQ ID NOs for each disclosed sequence is also indicated in Table 1.
  • HM polypeptide refers to a full-length HM protein or a functionally active fragment or derivative thereof.
  • a "functionally active" HM fragment or derivative exhibits one or more functional activities associated with a full-length, wild-type HM protein, such as antigenic or immunogenic activity, ability to bind natural cellular substrates, etc.
  • the functional activity of HM proteins, derivatives and fragments can be assayed by various methods known to one skilled in the art (Current Protocols in Protein Science (1998) Coligan et al., eds., John Wiley & Sons, Inc., Somerset, New Jersey) and as further discussed below.
  • a functionally active HM polypeptide is an HM derivative capable of rescuing defective endogenous HM activity, such as in cell based or animal assays; the rescuing derivative may be from the same or a different species.
  • functionally active fragments also include those fragments that comprise one or more structural domains of an HM, such as a binding domain. Protein domains can be identified using the PFAM program (Bateman A., et al., Nucleic Acids Res, 1999, 27:260-2). Methods for obtaining HM polypeptides are also further described below.
  • preferred fragments are functionally active, domain-containing fragments comprising at least 25 contiguous amino acids, preferably at least 50, more preferably 75, and most preferably at least 100 contiguous amino acids of any one of SEQ ID NOs: 15-28 (an HM). In further preferred embodiments, the fragment comprises the entire functionally active domain.
  • HM nucleic acid refers to a DNA or RNA molecule that encodes an HM polypeptide.
  • the HM polypeptide or nucleic acid or fragment thereof is from a human, but can also be an ortholog, or derivative thereof with at least 70% sequence identity, preferably at least 80%, more preferably 85%, still more preferably 90%, and most preferably at least 95% sequence identity with human HM.
  • Methods of identifying orthlogs are known in the art. Normally, orthologs in different species retain the same function, due to presence of one or more protein motifs and/or 3-dimensional structures. Orthologs are generally identified by sequence homology analysis, such as BLAST analysis, usually using protein bait sequences.
  • Sequences are assigned as a potential ortholog if the best hit sequence from the forward BLAST result retrieves the original query sequence in the reverse BLAST (Huynen MA and Bork P, Proc Natl Acad Sci (1998) 95:5849-5856; Huynen MA et al, Genome Research (2000) 10:1204-1210).
  • Programs for multiple sequence alignment such as CLUSTAL (Thompson JD et al, 1994, Nucleic Acids Res 22:4673-4680) may be used to highlight conserved regions and/or residues of orthologous proteins and to generate phylogenetic trees.
  • orthologous sequences from two species generally appear closest on the tree with respect to all other sequences from these two species.
  • Structural threading or other analysis of protein folding e.g., using software by ProCeryon, Biosciences, Salzburg, Austria
  • a gene duplication event follows speciation, a single gene in one species, such as Drosophila, may correspond to multiple genes (paralogs) in another, such as human.
  • the term "orthologs" encompasses paralogs.
  • percent (%) sequence identity with respect to a subject sequence, or a specified portion of a subject sequence, is defined as the percentage of nucleotides or amino acids in the candidate derivative sequence identical with the nucleotides or amino acids in the subject sequence (or specified portion thereof), after aligning the sequences and introducing gaps, if necessary to achieve the maximum percent sequence identity, as generated by the program WU- BLAST-2.0al9 (Altschul et al, J. Mol. Biol. (1997) 215:403-410) with all the search parameters set to default values.
  • the HSP S and HSP S2 parameters are dynamic values and are established by the program itself depending upon the composition of the particular sequence and composition of the particular database against which the sequence of interest is being searched.
  • a % identity value is determined by the number of matching identical nucleotides or amino acids divided by the sequence length for which the percent identity is being reported. "Percent (%) amino acid sequence similarity" is determined by doing the same calculation as for determining % amino acid sequence identity, but including conservative amino acid substitutions in addition to identical amino acids in the computation.
  • Aromatic amino acids that can be substituted for each other are phenylalanine, tryptophan, and tyrosine; interchangeable hydrophobic amino acids are leucine, isoleucine, methionine, and valine; interchangeable polar amino acids are glutamine and asparagine; interchangeable basic amino acids are arginine, lysine and histidine; interchangeable acidic amino acids are aspartic acid and glutamic acid; and interchangeable small amino acids are alanine, serine, threonine, cysteine and glycine.
  • an alignment for nucleic acid sequences is provided by the local homology algorithm of Smith and Waterman (Smith and Waterman, 1981, Advances in Applied Mathematics 2:482-489; database: European Bioinformatics Institute; Smith and Waterman, 1981, J. of Molec.Biol., 147:195-197; Nicholas et al., 1998, "A tutorial on Searching Sequence Databases and Sequence Scoring Methods” (www.psc.edu) and references cited therein.; W.R. Pearson, 1991, Genomics 11:635-650).
  • This algorithm can be applied to amino acid sequences by using the scoring matrix developed by Dayhoff (Dayhoff: Atlas of Protein Sequences and Structure, M. O. Dayhoff ed., 5 suppl.
  • Derivative nucleic acid molecules of the subject nucleic acid molecules include sequences that hybridize to the nucleic acid sequence of any of SEQ ID NOs: 1-14.
  • the stringency of hybridization can be controlled by temperature, ionic strength, pH, and the presence of denaturing agents such as formamide during hybridization and washing. Conditions routinely used are set out in readily available procedure texts (e.g., Current Protocol in Molecular Biology, Vol. 1, Chap. 2.10, John Wiley & Sons, Publishers (1994); Sambrook et ah, Molecular Cloning, Cold Spring Harbor (1989)).
  • a nucleic acid molecule of the invention is capable of hybridizing to a nucleic acid molecule containing the nucleotide sequence of any one of SEQ ID NOs:l-14 under high stringency hybridization conditions that are: prehybridization of filters containing nucleic acid for 8 hours to overnight at 65° C in a solution comprising 6X single strength citrate (SSC) (IX SSC is 0.15 M NaCl, 0.015 M Na citrate; pH 7.0), 5X Denhardt's solution, 0.05% sodium pyrophosphate and 100 ⁇ g/ml herring sperm DNA; hybridization for 18-20 hours at 65° C in a solution containing 6X SSC, IX Denhardt's solution, 100 ⁇ g/ml yeast tRNA and 0.05% sodium pyrophosphate; and washing of filters at 65° C for lh in a solution containing 0.1X SSC and 0.1% SDS (sodium dodecyl sulfate).
  • SSC single strength
  • moderately stringent hybridization conditions comprise: pretreatment of filters containing nucleic acid for 6 h at 40° C in a solution containing 35% formamide, 5X SSC, 50 mM Tris-HCl ( ⁇ H7.5), 5mM EDTA, 0.1% PVP, 0.1% Ficoll, 1% BSA, and 500 ⁇ g/ml denatured salmon sperm DNA; hybridization for 18-20h at 40° C in a solution containing 35% formamide, 5X SSC, 50 mM Tris-HCl (pH7.5), 5mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.2% BSA, 100 ⁇ g/ml salmon sperm DNA, and 10% (wt/vol) dextran sulfate; followed by washing twice for 1 hour at 55° C in a solution containing 2X SSC and 0.1% SDS.
  • low stringency conditions can be used that comprise: incubation for 8 hours to overnight at 37° C in a solution comprising 20% formamide, 5 x SSC, 50 mM sodium phosphate (pH 7.6), 5X Denhardt's solution, 10% dextran sulfate, and 20 ⁇ g/ml denatured sheared salmon sperm DNA; hybridization in the same buffer for 18 to 20 hours; and washing of filters in 1 x SSC at about 37° C for 1 hour.
  • HM nucleic acids and polypeptides useful for identifying and testing agents that modulate HM function and for other applications related to the involvement of HM in the p53 pathway.
  • HM nucleic acids and derivatives and orthologs thereof may be obtained using any available method. For instance, techniques for isolating cDNA or genomic DNA sequences of interest by screening DNA libraries or by using polymerase chain reaction (PCR) are well known in the art.
  • PCR polymerase chain reaction
  • the particular use for the protein will dictate the particulars of expression, production, and purification methods. For instance, production of proteins for use in screening for modulating agents may require methods that preserve specific biological activities of these proteins, whereas production of proteins for antibody generation may require structural integrity of particular epitopes.
  • HM protein to be purified for screening or antibody production may require the addition of specific tags (e.g., generation of fusion proteins).
  • tags e.g., generation of fusion proteins.
  • Overexpression of an HM protein for assays used to assess HM function, such as involvement in cell cycle regulation or hypoxic response, may require expression in eukaryotic cell lines capable of these cellular activities.
  • recombinant HM is expressed in a cell line known to have defective p53 function (e.g. SAOS-2 osteoblasts, H1299 lung cancer cells, C33A and HT3 cervical cancer cells, HT-29 and DLD-1 colon cancer cells, among others, available from American Type Culture Collection (ATCC), Manassas, VA).
  • ATCC American Type Culture Collection
  • VA Manassas
  • the nucleotide sequence encoding an HM polypeptide can be inserted into any appropriate expression vector.
  • the necessary transcriptional and translational signals, including promoter/enhancer element, can derive from the native HM gene andor its flanking regions or can be heterologous.
  • a variety of host- vector expression systems may be utilized, such as mammalian cell systems infected with virus (e.g. vaccinia virus, adenovirus, etc.); insect cell systems infected with virus (e.g. baculovirus); microorganisms such as yeast containing yeast vectors, or bacteria transformed with bacteriophage, plasmid, or cosmid DNA.
  • An isolated host cell strain that modulates the expression of, modifies, and/or specifically processes the gene product may be used.
  • the expression vector can comprise a promoter operably linked to an HM gene nucleic acid, one or more origins of replication, and, one or more selectable markers (e.g. thymidine kinase activity, resistance to antibiotics, etc.).
  • selectable markers e.g. thymidine kinase activity, resistance to antibiotics, etc.
  • recombinant expression vectors can be identified by assaying for the expression of the HM gene product based on the physical or functional properties of the HM protein in in vitro assay systems (e.g. immunoassays).
  • the HM protein, fragment, or derivative may be optionally expressed as a fusion, or chimeric protein product (i.e. it is joined via a peptide bond to a heterologous protein sequence of a different protein), for example to facilitate purification or detection.
  • a chimeric product can be made by ligating the appropriate nucleic acid sequences encoding the desired amino acid sequences to each other using standard methods and expressing the chimeric product.
  • a chimeric product may also be made by protein synthetic techniques, e.g. by use of a peptide synthesizer (Hunkapiller et al, Nature (1984) 310:105-111).
  • the gene product can be isolated and purified using standard methods (e.g. ion exchange, affinity, and gel exclusion chromatography; centrifugation; differential solubility; electrophoresis).
  • native HM proteins can be purified from natural sources, by standard methods (e.g. immunoaffinity purification).
  • a protein Once a protein is obtained, it may be quantified and its activity measured by appropriate methods, such as immunoassay, bioassay, or other measurements of physical properties, such as crystallography.
  • mis-expression encompasses ectopic expression, over-expression, under- expression, and non-expression (e.g. by gene knock-out or blocking expression that would otherwise normally occur).
  • Animal models that have been genetically modified to alter HM expression may be used in in vivo assays to test for activity of a candidate p53 modulating agent, or to further assess the role of HM in a p53 pathway process such as apoptosis or cell proliferation.
  • the altered HM expression results in a detectable phenotype, such as decreased or increased levels of cell proliferation, angiogenesis, or apoptosis compared to control animals having normal HM expression.
  • the genetically modified animal may additionally have altered p53 expression (e.g. p53 knockout).
  • Preferred genetically modified animals are mammals such as primates, rodents (preferably mice or rats), among others.
  • Preferred non-mammalian species include zebrafish, C.
  • Preferred genetically modified animals are transgenic animals having a heterologous nucleic acid sequence present as an extracliromosomal element in a portion of its cells, i.e. mosaic animals (see, for example, techniques described by Jakobovits, 1994, Curr. Biol. 4:761- 763.) or stably integrated into its germ line DNA (i.e., in the genomic sequence of most or all of its cells).
  • Heterologous nucleic acid is introduced into the germ line of such transgenic animals by genetic manipulation of, for example, embryos or embryonic stem cells of the host animal.
  • transgenic mice see Brinster et al., Proc. Nat. Acad. Sci. USA 82: 4438-4442 (1985), U.S. Pat. Nos. 4,736,866 and 4,870,009, both by Leder et al., U.S. Pat. No. 4,873,191 by Wagner et al., and Hogan, B., Manipulating the Mouse Embryo, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., (1986); for particle bombardment see U.S. Pat.
  • Clones of the nonhuman transgenic animals can be produced according to available methods (see Wilmut, I. et al. (1991) Nature 385:810-813; and PCT International Publication Nos. WO 97/07668 and WO 97/07669).
  • the transgenic animal is a "knock-out" animal having a heterozygous or homozygous alteration in the sequence of an endogenous HM gene that results in a decrease of HM function, preferably such that HM expression is undetectable or insignificant.
  • Knock-out animals are typically generated by homologous recombination with a vector comprising a transgene having at least a portion of the gene to be knocked out. Typically a deletion, addition or substitution has been introduced into the transgene to functionally disrupt it.
  • the transgene can be a human gene (e.g., from a human genomic clone) but more preferably is an ortholog of the human gene derived from the transgenic host species.
  • a mouse HM gene is used to construct a homologous recombination vector suitable for altering an endogenous HM gene in the mouse genome.
  • homologous recombination in mice are available (see Capecchi, Science (1989) 244:1288-1292; Joyner et al, Nature (1989) 338:153-156). Procedures for the production of non-rodent transgenic mammals and other animals are also available (Houdebine and Chourrout, supra; Pursel et al., Science (1989) 244:1281-1288; Simms et al, Bio/Technology (1988) 6:179-183).
  • knock-out animals such as mice harboring a knockout of a specific gene, may be used to produce antibodies against the human counterpart of the gene that has been knocked out (Claesson MH et al., (1994) Scan J Immunol 40:257-264; Declerck PJ et al., (1995) J Biol Chem. 270:8397-400).
  • the transgenic animal is a "knock-in" animal having an alteration in its genome that results in altered expression (e.g., increased (including ectopic) or decreased expression) of the HM gene, e.g., by introduction of additional copies of HM, or by operatively inserting a regulatory sequence that provides for altered expression of an endogenous copy of the HM gene.
  • a regulatory sequence include inducible, tissue-specific, and constitutive promoters and enhancer elements.
  • the knock- in can be homozygous or heterozygous.
  • Transgenic nonhuman animals can also be produced that contain selected systems allowing for regulated expression of the transgene.
  • a system that may be produced is the cre/loxP recombinase system of bacteriophage PI (Lakso et al, PNAS (1992) 89:6232-6236; U.S. Pat. No. 4,959,317). If a cre/loxP recombinase system is used to regulate expression of the transgene, animals containing transgenes encoding both the Cre recombinase and a selected protein are required.
  • Such animals can be provided through the construction of "double" transgenic animals, e.g., by mating two transgenic animals, one containing a transgene encoding a selected protein and the other containing a transgene encoding a recombinase.
  • a recombinase system is the FLP recombinase system of Saccharomyces cerevisiae (O'Gorman et al. (1991) Science 251:1351-1355; U.S. Pat. No. 5,654,182).
  • both Cre-LoxP and Flp-Frt are used in the same system to regulate expression of the transgene, and for sequential deletion of vector sequences in the same cell (Sun X et al (2000) Nat Genet 25:83-6).
  • the genetically modified animals can be used in genetic studies to further elucidate the p53 pathway, as animal models of disease and disorders implicating defective p53 function, and for in vivo testing of candidate therapeutic agents, such as those identified in screens described below.
  • the candidate therapeutic agents are administered to a genetically modified animal having altered HM function and phenotypic changes are compared with appropriate control animals such as genetically modified animals that receive placebo treatment, and/or animals with unaltered HM expression that receive candidate therapeutic agent.
  • animal models having defective p53 function (and otherwise normal HM function)
  • a p53 knockout mouse can be used to assess, in vivo, the activity of a candidate p53 modulating agent identified in one of the in vitro assays described below.
  • p53 knockout mice are described in the literature (Jacks et al., Nature 2001;410:1111-1116, 1043-1044; Donehower et al., supra).
  • the candidate p53 modulating agent when administered to a model system with cells defective in p53 function, produces a detectable phenotypic change in the model system indicating that the p53 function is restored, i.e., the cells exhibit normal cell cycle progression.
  • the invention provides methods to identify agents that interact with and/or modulate the function of HM and/or the p53 pathway. Modulating agents identified by the methods are also part of the invention. Such agents are useful in a variety of diagnostic and therapeutic applications associated with the p53 pathway, as well as in further analysis of the HM protein and its contribution to the p53 pathway. Accordingly, the invention also provides methods for modulating the p53 pathway comprising the step of specifically modulating HM activity by administering an HM-interacting or -modulating agent.
  • an "HM-modulating agent” is any agent that modulates HM function, for example, an agent that interacts with HM to inhibit or enhance HM activity or otherwise affect normal HM function.
  • HM function can be affected at any level, including transcription, protein expression, protein localization, and cellular or extra-cellular activity.
  • the HM - modulating agent specifically modulates the function of the HM.
  • the phrases "specific modulating agent”, “specifically modulates”, etc., are used herein to refer to modulating agents that direcfly bind to the HM polypeptide or nucleic acid, and preferably inhibit, enhance, or otherwise alter, the function of the HM. These phrases also encompasses modulating agents that alter the interaction of the HM with a binding partner, substrate, or cofactor (e.g. by binding to a binding partner of an HM, or to a protein/binding partner complex, and altering HM function).
  • the HM- modulating agent is a modulator of the p53 pathway (e.g. it restores and/or upregulates p53 function) and thus is also a p53- modulating agent.
  • Preferred HM-modulating agents include small molecule compounds; HM-interacting proteins, including antibodies and other biotherapeutics; and nucleic acid modulators such as antisense and RNA inhibitors.
  • the modulating agents may be formulated in pharmaceutical compositions, for example, as compositions that may comprise other active ingredients, as in combination therapy, and/or suitable carriers or excipients. Techniques for formulation and administration of the compounds may be found in "Remington's Pharmaceutical Sciences” Mack Publishing Co., Easton, PA, 19 th edition.
  • Small molecule modulators Small molecules are often preferred to modulate function of proteins with enzymatic function, and/or containing protein interaction domains.
  • Chemical agents referred to in the art as "small molecule” compounds are typically organic, non-peptide molecules, having a molecular weight less than 10,000, preferably less than 5,000, more preferably less than 1,000, and most preferably less than 500.
  • This class of modulators includes chemically synthesized molecules, for instance, compounds from combinatorial chemical libraries. Synthetic compounds may be rationally designed or identified based on known or inferred properties of the HM protein or may be identified by screening compound libraries.
  • modulators of this class are natural products, particularly secondary metabolites from organisms such as plants or fungi, which can also be identified by screening compound libraries for HM-modulating activity. Methods for generating and obtaining compounds are well known in the art (Schreiber SL, Science (2000) 151: 1964-1969; Radmann J and Gunther J, Science (2000) 151:1947-1948).
  • Small molecule modulators identified from screening assays, as described below, can be used as lead compounds from which candidate clinical compounds may be designed, optimized, and synthesized. Such clinical compounds may have utility in treating pathologies associated with the p53 pathway.
  • the activity of candidate small molecule modulating agents may be improved several-fold through iterative secondary functional validation, as further described below, structure determination, and candidate modulator modification and testing.
  • candidate clinical compounds are generated with specific regard to clinical and pharmacological properties.
  • the reagents may be derivatized and re-screened using in vitro and in vivo assays to optimize activity and minimize toxicity for pharmaceutical development. Protein Modulators
  • HM-interacting proteins are useful in a variety of diagnostic and therapeutic applications related to the p53 pathway and related disorders, as well as in validation assays for other HM-modulating agents.
  • HM-interacting proteins affect normal HM function, including transcription, protein expression, protein localization, and cellular or extra-cellular activity.
  • HM- interacting proteins are useful in detecting and providing information about the function of HM proteins, as is relevant to p53 related disorders, such as cancer (e.g., for diagnostic means).
  • An HM-interacting protein may be endogenous, i.e. one that naturally interacts genetically or biochemically with an HM, such as a member of the HM pathway that modulates HM expression, localization, and/or activity.
  • HM-modulators include dominant negative forms of HM-interacting proteins and of HM proteins themselves.
  • Yeast two- hybrid and variant screens offer preferred methods for identifying endogenous HM- interacting proteins (Finley, R. L. et al. (1996) in DNA Cloning-Expression Systems: A Practical Approach, eds. Glover D. & Hames B. D (Oxford University Press, Oxford, England), pp. 169-203; Fashema SF et al., Gene (2000) 250:1-14; Drees BL Curr Opin Chem Biol (1999) 3:64-70; Vidal M and Legrain P Nucleic Acids Res (1999) 27:919-29; and U.S. Pat. No.
  • Mass spectrometry is an alternative preferred method for the elucidation of protein complexes (reviewed in, e.g., Pandley A and Mann M, Nature (2000) 405:837-846; Yates JR 3 rd , Trends Genet (2000) 16:5-8).
  • An HM-interacting protein may be an exogenous protein, such as an HM-specific antibody or a T-cell antigen receptor (see, e.g., Harlow and Lane (1988) Antibodies, A Laboratory Manual, Cold Spring Harbor Laboratory; Harlow and Lane (1999) Using antibodies: a laboratory manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press). HM antibodies are further discussed below. hi preferred embodiments, an HM-interacting protein specifically binds an HM protein. In alternative preferred embodiments, an HM-modulating agent binds an HM substrate, binding partner, or cofactor.
  • the protein modulator is an HM specific antibody agonist or antagonist.
  • the antibodies have therapeutic and diagnostic utilities, and can be used in screening assays to identify HM modulators.
  • the antibodies can also be used in dissecting the portions of the HM pathway responsible for various cellular responses and in the general processing and maturation of the HM.
  • Antibodies that specifically bind HM polypeptides can be generated using known methods.
  • the antibody is specific to a mammalian ortholog of HM polypeptide, and more preferably, to human HM.
  • Antibodies may be polyclonal, monoclonal (mAbs), humanized or chimeric antibodies, single chain antibodies, Fab fragments, F(ab').sub.2 fragments, fragments produced by a FAb expression library, anti-idiotypic (anti-Id) antibodies, and epitope-binding fragments of any of the above.
  • HM which are particularly antigenic
  • epitopes of HM which are particularly antigenic can be selected, for example, by routine screening of HM polypeptides for antigenicity or by applying a theoretical method for selecting antigenic regions of a protein (Hopp and Wood (1981), Proc. Nati. Acad. Sci. U.S.A. 78:3824-28; Hopp and Wood, (1983) Mol. Immunol. 20:483-89; Sutcliffe et al., (1983) Science 219:660-66) to the amino acid sequence shown in any of SEQ ID NOs: 15-28.
  • Monoclonal antibodies with affinities of IO 8 M "1 preferably IO 9 M "1 to IO 10 M "1 , or stronger can be made by standard procedures as described (Harlow and Lane, supra; Goding (1986)
  • Antibodies may be generated against crude cell extracts of HM or substantially purified fragments thereof. If HM fragments are used, they preferably comprise at least 10, and more preferably, at least 20 contiguous amino acids of an HM protein. In a particular embodiment, HM-specific antigens and/or immunogens are coupled to carrier proteins that stimulate the immune response.
  • the subject polypeptides are covalently coupled to the keyhole limpet hemocyanin (KLH) carrier, and the conjugate is emulsified in Freund's complete adjuvant, which enhances the immune response.
  • KLH keyhole limpet hemocyanin
  • An appropriate immune system such as a laboratory rabbit or mouse is immunized according to conventional protocols.
  • HM-specific antibodies is assayed by an appropriate assay such as a solid phase enzyme-linked immunosorbant assay (ELISA) using immobilized corresponding HM polypeptides.
  • an appropriate assay such as a solid phase enzyme-linked immunosorbant assay (ELISA) using immobilized corresponding HM polypeptides.
  • Other assays such as radioimmunoassays or fluorescent assays might also be used.
  • Chimeric antibodies specific to HM polypeptides can be made that contain different portions from different animal species. For instance, a human immunoglobulin constant region may be linked to a variable region of a murine mAb, such that the antibody derives its biological activity from the human antibody, and its binding specificity from the murine fragment. Chimeric antibodies are produced by splicing together genes that encode the appropriate regions from each species (Morrison et al., Proc. Nati. Acad. Sci.
  • Humanized antibodies which are a form of chimeric antibodies, can be generated by grafting complementary-determining regions (CDRs) (Carlos, T. M., J. M. Harlan. 1994. Blood 84:2068-2101) of mouse antibodies into a background of human framework regions and constant regions by recombinant DNA technology (Riechmann LM, et al., 1988 Nature 323: 323-327). Humanized antibodies contain -10% murine sequences and ⁇ 90% human sequences, and thus further reduce or eliminate immunogenicity, while retaining the antibody specificities (Co MS, and Queen C. 1991 Natore 351: 501-501; Morrison SL. 1992 Ann. Rev. Immun. 10:239-265). Humanized antibodies and methods of their production are well-known in the art (U.S. Pat. Nos. 5,530,101, 5,585,089, 5,693,762, and 6,180,370).
  • HM-specific single chain antibodies which are recombinant, single chain polypeptides formed by linking the heavy and light chain fragments of the Fv regions via an amino acid bridge, can be produced by methods known in the art (U.S. Pat. No. 4,946,778; Bird, Science (1988) 242:423-426; Huston et al, Proc. Natl. Acad. Sci. USA (1988) 85:5879- 5883; and Ward et al., Nature (1989) 334:544-546).
  • T-cell antigen receptors are included within the scope of antibody modulators (Harlow and Lane, 1988, supra).
  • polypeptides and antibodies of the present invention may be used with or without modification. Frequently, antibodies will be labeled by joining, either covalently or non- covalently, a substance that provides for a detectable signal, or that is toxic to cells that express the targeted protein (Menard S, et al., Int J. Biol Markers (1989) 4:131-134).
  • labels and conjugation techniques are known and are reported extensively in both the scientific and patent literature. Suitable labels include radionuclides, enzymes, substrates, cofactors, inhibitors, fluorescent moieties, fluorescent emitting lanthanide metals, chemiluminescent moieties, bioluminescent moieties, magnetic particles, and the like (U.S. Pat. Nos.
  • the antibodies of the subject invention are typically administered parenterally, when possible at the target site, or intravenously.
  • the therapeutically effective dose and dosage regimen is determined by clinical studies.
  • the amount of antibody administered is in the range of about 0.1 mg/kg -to about 10 mg/kg of patient weight.
  • the antibodies are formulated in a unit dosage injectable form (e.g., solution, suspension, emulsion) in association with a pharmaceutically acceptable vehicle.
  • a pharmaceutically acceptable vehicle are inherently nontoxic and non-therapeutic. Examples are water, saline, Ringer's solution, dextrose solution, and 5% human serum albumin.
  • Nonaqueous vehicles such as fixed oils, ethyl oleate, or liposome carriers may also be used.
  • the vehicle may contain minor amounts of additives, such as buffers and preservatives, which enhance isotonicity and chemical stability or otherwise enhance therapeutic potential.
  • the antibodies' concentrations in such vehicles are typically in the range of about 1 mg ml to aboutlO mg/ml.
  • an HM-interacting protein may have biotherapeutic applications.
  • Biotherapeutic agents formulated in pharmaceutically acceptable carriers and dosages may be used to activate or inhibit signal transduction pathways. This modulation may be accomplished by binding a ligand, thus inhibiting the activity of the pathway; or by binding a receptor, either to inhibit activation of, or to activate, the receptor.
  • the biotherapeutic may itself be a ligand capable of activating or inhibiting a receptor. Biotherapeutic agents and methods of producing them are described in detail in U.S. Pat. No. 6,146,628.
  • HM When the HM is a ligand, it may be used as a biotherapeutic agent to activate or inhibit its natural receptor. Alternatively, antibodies against HM, as described in the previous section, may be used as biotherapeutic agents.
  • HM When the HM is a receptor, its ligand(s), antibodies to the ligand(s) or the HM itself may be used as biotherapeutics to modulate the activity of HM in the p53 pathway.
  • Nucleic Acid Modulators When the HM is a receptor, its ligand(s), antibodies to the ligand(s) or the HM itself may be used as biotherapeutics to modulate the activity of HM in the p53 pathway.
  • HM-modulating agents comprise nucleic acid molecules, such as antisense oligomers or double stranded RNA (dsRNA), which generally inhibit HM activity.
  • Preferred nucleic acid modulators interfere with the function of the HM nucleic acid such as DNA replication, transcription, translocation of the HM RNA to the site of protein translation, translation of protein from the HM RNA, splicing of the HM RNA to yield one or more mRNA species, or catalytic activity which may be engaged in or facilitated by the HM RNA.
  • the antisense oligomer is an oligonucleotide that is sufficiently complementary to an HM mRNA to bind to and prevent translation, preferably by binding to the 5' untranslated region.
  • HM-specific antisense oligonucleotides preferably range from at least 6 to about 200 nucleotides.
  • the oligonucleotide is preferably at least 10, 15, or 20 nucleotides in length.
  • the oligonucleotide is preferably less than 50, 40, or 30 nucleotides in length.
  • the oligonucleotide can be DNA or RNA or a chimeric mixture or derivatives or modified versions thereof, single-stranded or double-stranded.
  • the oligonucleotide can be modified at the base moiety, sugar moiety, or phosphate backbone.
  • the oligonucleotide may include other appending groups such as peptides, agents that facilitate transport across the cell membrane, hybridization-triggered cleavage agents, and intercalating agents.
  • the antisense oligomer is a phosphothioate morpholino oligomer (PMO).
  • PMOs are assembled from four different morpholino subunits, each of which contain one of four genetic bases (A, C, G, or T) linked to a six-membered morpholine ring. Polymers of these subunits are joined by non-ionic phosphodiamidate intersubunit linkages. Details of how to make and use PMOs and other antisense oligomers are well known in the art (e.g. see WO99/18193; Probst JC, Antisense
  • RNAi is the process of sequence-specific, post- transcriptional gene silencing in animals and plants, initiated by double-stranded RNA (dsRNA) that is homologous in sequence to the silenced gene.
  • dsRNA double-stranded RNA
  • Methods relating to the use of RNAi to silence genes in C. elegans, Drosophila, plants, and humans are known in the art (Fire A, et al., 1998 Nature 391:806-811; Fire, A. Trends Genet. 15, 358-363 (1999); Sharp, P. A. RNA interference 2001. Genes Dev. 15, 485-490 (2001); Hammond, S.
  • Nucleic acid modulators are commonly used as research reagents, diagnostics, and therapeutics. For example, antisense oligonucleotides, which are able to inhibit gene expression with seventeen specificity, are often used to elucidate the function of particular genes (see, for example, U.S. Pat. No. 6,165,790). Nucleic acid modulators are also used, for example, to distinguish between functions of various members of a biological pathway.
  • antisense oligomers have been employed as therapeutic moieties in the treatment of disease states in animals and man and have been demonstrated in numerous clinical trials to be safe and effective (Milligan JF, et al, Current Concepts in Antisense Drug Design, J Med Chem. (1993) 36: 1923-1937; Tonkinson JL et al, Antisense
  • an HM-specific nucleic acid modulator is used in an assay to further elucidate the role of the HM in the p53 pathway, and/or its relationship to other members of the pathway.
  • an HM- specific antisense oligomer is used as a therapeutic agent for treatment of p53-related disease states.
  • an "assay system” encompasses all the components required for performing and analyzing results of an assay that detects and/or measures a particular event.
  • primary assays are used to identify or confirm a modulator's specific biochemical or molecular effect with respect to the HM nucleic acid or protein.
  • secondary assays further assess the activity of an HM modulating agent identified by a primary assay and may confirm that the modulating agent affects HM in a manner relevant to the p53 pathway. In some cases, HM modulators will be directly tested in a secondary assay.
  • the screening method comprises contacting a suitable assay system comprising an HM polypeptide or nucleic acid with a candidate agent under conditions whereby, but for the presence of the agent, the system provides a reference activity (e.g. binding activity), which is based on the particular molecular event the screening method detects.
  • a reference activity e.g. binding activity
  • a statistically significant difference between the agent-biased activity and the reference activity indicates that the candidate agent modulates HM activity, and hence the p53 pathway.
  • the HM polypeptide or nucleic acid used in the assay may comprise any of the nucleic acids or polypeptides described above.
  • the type of modulator tested generally determines the type of primary assay.
  • screening assays are used to identify candidate modulators. Screening assays may be cell-based or may use a cell-free system that recreates or retains the relevant biochemical reaction of the target protein (reviewed in Sittampalam GS et al., Curr Opin Chem Biol (1997) 1:384-91 and accompanying references).
  • the term "cell-based” refers to assays using live cells, dead cells, or a particular cellular fraction, such as a membrane, endoplasmic reticulum, or mitochondrial fraction.
  • cell free encompasses assays using substantially purified protein (either endogenous or recombinantly produced), partially purified or crude cellular extracts.
  • Screening assays may detect a variety of molecular events, including protein-DNA interactions, protein-protein interactions (e.g., receptor-ligand binding), transcriptional activity (e.g., using a reporter gene), enzymatic activity (e.g., via a property of the substrate), activity of second messengers, immunogenicty and changes in cellular morphology or other cellular characteristics.
  • Appropriate screening assays may use a wide range of detection methods including fluorescent, radioactive, colorimetric, spectrophotometric, and amperometric methods, to provide a read-out for the particular molecular event detected.
  • HM-based screening assays usually require systems for recombinant expression of HM and any auxiliary proteins demanded by the particular assay.
  • Appropriate methods for generating recombinant proteins produce sufficient quantities of proteins that retain their relevant biological activities and are of sufficient purity to optimize activity and assure assay reproducibility.
  • Yeast two-hybrid and variant screens, and mass spectrometry provide preferred methods for determining protein-protein interactions and elucidation of protein complexes.
  • the binding specificity of the interacting protein to the HM protein may be assayed by various known methods such as substrate processing (e.g.
  • binding equilibrium constants usually at least about IO 7 M "1 , preferably at least about 10 8 M “1 , more preferably at least about IO 9 M "1
  • immunogenicity e.g. ability to elicit HM specific antibody in a heterologous host such as a mouse, rat, goat or rabbit.
  • binding may be assayed by, respectively, substrate and ligand processing.
  • the screening assay may measure a candidate agent's ability to specifically bind to or modulate activity of an HM polypeptide, a fusion protein thereof, or to cells or membranes bearing the polypeptide or fusion protein.
  • the HM polypeptide can be full length or a fragment thereof that retains functional HM activity.
  • the HM polypeptide may be fused to another polypeptide, such as a peptide tag for detection or anchoring, or to another tag.
  • the HM polypeptide is preferably human HM, or is an ortholog or derivative thereof as described above.
  • the screening assay detects candidate agent- based modulation of HM interaction with a binding target, such as an endogenous or exogenous protein or other substrate that has HM -specific binding activity, and can be used to assess normal HM gene function.
  • a binding target such as an endogenous or exogenous protein or other substrate that has HM -specific binding activity
  • screening assays are high throughput or ultra high throughput and thus provide automated, cost-effective means of screening compound libraries for lead compounds (Fernandes PB, Curr Opin Chem Biol (1998) 2:597-603; Sundberg SA, Curr Opin Biotechnol 2000, 11:47-53).
  • screening assays uses fluorescence technologies, including fluorescence polarization, time-resolved fluorescence, and fluorescence resonance energy transfer.
  • Protein phosphatase assays Protein phosophatases catalyze the removal of a gamma phosphate from a serine, threonine or tyrosine residue in a protein substrate.
  • phosphatases act in opposition to kinases, appropriate assays measure the same parameters as kinase assays, i one example, the dephosphorylation of a fluorescently labeled peptide substrate allows trypsin cleavage of the substrate, which in turn renders the cleaved substrate significantly more fluorescent (Nishikata M et al, Biochem J (1999) 343:35- 391).
  • fluorescence polarization a solution-based, homogeneous technique requiring no immobilization or separation of reaction components, is used to develop high throughput screening (HTS) assays for protein phosphatases.
  • This assay uses direct binding of the phosphatase with the target, and increasing concentrations of target- phosphatase increase the rate of dephosphorylation, leading to a change in polarization (Parker GJ et al., (2000) J Biomol Screen 5:77-88).
  • Apoptosis assays may be performed by terminal deoxynucleotidyl transferase-mediated digoxigenin- 11 -dUTP nick end labeling (TUNEL) assay.
  • TUNEL terminal deoxynucleotidyl transferase-mediated digoxigenin- 11 -dUTP nick end labeling
  • the TUNEL assay is used to measure nuclear DNA fragmentation characteristic of apoptosis ( Lazebnik et al , 1994, Nature 371, 346), by following the incorporation of fluorescein-dUTP (Yonehara et al, 1989, J. Exp. Med. 169, 1747).
  • Apoptosis may further be assayed by acridine orange staining of tissue culture cells (Lucas, R., et al., 1998, Blood 15:4730-41).
  • An apoptosis assay system may comprise a cell that expresses an HM, and that optionally has defective p53 function (e.g. p53 is over-expressed or under-expressed relative to wild- type cells).
  • a test agent can be added to the apoptosis assay system and changes in induction of apoptosis relative to controls where no test agent is added, identify candidate p53 modulating agents.
  • an apoptosis assay may be used as a secondary assay to test a candidate p53 modulating agents that is initially identified using a cell-free assay system.
  • An apoptosis assay may also be used to test whether HM function plays a direct role in apoptosis.
  • an apoptosis assay may be performed on cells that over- or under-express HM relative to wild type cells. Differences in apoptotic response compared to wild type cells suggests that the HM plays a direct role in the apoptotic response. Apoptosis assays are described further in US Pat. No. 6,133,437.
  • Cell proliferation and cell cycle assays may be assayed via bromodeoxyuridine (BRDU) incorporation.
  • BRDU bromodeoxyuridine
  • This assay identifies a cell population undergoing DNA synthesis by inco ⁇ oration of BRDU into newly-synthesized DNA. Newly-synthesized DNA may then be detected using an anti-BRDU antibody (Hoshino et al, 1986, Int. J. Cancer 38, 369; Campana etal, 1988, J. Immunol. Meth. 107, 79), or by other means.
  • Cell Proliferation may also be examined using [ H] -thymidine incorporation (Chen, J.,
  • Another proliferation assay uses the dye Alamar Blue (available from Biosource International), which fluoresces when reduced in living cells and provides an indirect measurement of cell number (Voytik-Harbin SL et al., 1998, In Vitro Cell Dev Biol Anim 34:239-46).
  • Cell proliferation may also be assayed by colony formation in soft agar (Sambrook et al., Molecular Cloning, Cold Spring Harbor (1989)). For example, cells transformed with HM are seeded in soft agar plates, and colonies are measured and counted after two weeks incubation.
  • Involvement of a gene in the cell cycle may be assayed by flow cytometry (Gray JW et al. (1986) Int J Radiat Biol Relat Stud Phys Chem Med 49:237-55).
  • Cells transfected with an HM may be stained with propidium iodide and evaluated in a flow cytometer (available from Becton Dickinson), which indicates accumulation of cells in different stages of the cell cycle.
  • a cell proliferation or cell cycle assay system may comprise a cell that expresses an HM, and that optionally has defective p53 function (e.g. p53 is over- expressed or under-expressed relative to wild-type cells).
  • a test agent can be added to the assay system and changes in cell proliferation or cell cycle relative to controls where no test agent is added, identify candidate p53 modulating agents.
  • the cell proliferation or cell cycle assay may be used as a secondary assay to test a candidate p53 modulating agents that is initially identified using another assay system such as a cell-free assay system.
  • a cell proliferation assay may also be used to test whether HM function plays a direct role in cell proliferation or cell cycle.
  • a cell proliferation or cell cycle assay may be performed on cells that over- or under-express HM relative to wild type cells. Differences in proliferation or cell cycle compared to wild ' type cells suggests that the HM plays a direct role in cell proliferation or cell cycle.
  • Angiogenesis may be assayed using various human endothelial cell systems, such as umbilical vein, coronary artery, or dermal cells. Suitable assays include Alamar Blue based assays (available from Biosource International) to measure proliferation; migration assays using fluorescent molecules, such as the use of Becton Dickinson Falcon HTS FluoroBlock cell culture inserts to measure migration of cells through membranes in presence or absence of angiogenesis enhancer or suppressors; and tubule formation assays based on the formation of tubular structures by endothelial cells on Matrigel® (Becton Dickinson).
  • Alamar Blue based assays available from Biosource International
  • migration assays using fluorescent molecules such as the use of Becton Dickinson Falcon HTS FluoroBlock cell culture inserts to measure migration of cells through membranes in presence or absence of angiogenesis enhancer or suppressors
  • tubule formation assays based on the formation of tubular structures by endothelial cells on Ma
  • an angiogenesis assay system may comprise a cell that expresses an HM, and that optionally has defective p53 function (e.g. p53 is over-expressed or under-expressed relative to wild-type cells).
  • a test agent can be added to the angiogenesis assay system and changes in angiogenesis relative to controls where no test agent is added, identify candidate p53 modulating agents.
  • the angiogenesis assay may be used as a secondary assay to test a candidate p53 modulating agents that is initially identified using another assay system.
  • An angiogenesis assay may also be used to test whether HM function plays a direct role in cell proliferation.
  • an angiogenesis assay may be performed on cells that over- or under-express HM relative to wild type cells. Differences in angiogenesis compared to wild type cells suggests that the HM plays a direct role in angiogenesis.
  • hypoxia inducible factor-1 The alpha subunit of the transcription factor, hypoxia inducible factor-1 (HJF-l), is upregulated in tumor cells following exposure to hypoxia in vitro.
  • HIF-1 stimulates the expression of genes known to be important in tumour cell survival, such as those encoding glyolytic enzymes and VEGF.
  • Induction of such genes by hypoxic conditions may be assayed by growing cells transfected with HM in hypoxic conditions (such as with 0.1% O2, 5% CO2, and balance N2, generated in a Napco 7001 incubator (Precision Scientific)) and normoxic conditions, followed by assessment of gene activity or expression by Taqman®.
  • a hypoxic induction assay system may comprise a cell that expresses an HM, and that optionally has a mutated p53 (e.g. p53 is over-expressed or under-expressed relative to wild-type cells).
  • a test agent can be added to the hypoxic induction assay system and changes in hypoxic response relative to controls where no test agent is added, identify candidate p53 modulating agents.
  • the hypoxic induction assay may be used as a secondary assay to test a candidate p53 modulating agents that is initially identified using another assay system.
  • a hypoxic induction assay may also be used to test whether HM function plays a direct role in the hypoxic response.
  • a hypoxic induction assay may be performed on cells that over- or under- express HM relative to wild type cells. Differences in hypoxic response compared to wild type cells suggests that the HM plays a direct role in hypoxic induction.
  • Cell adhesion assays measure adhesion of cells to purified adhesion proteins, or adhesion of cells to each other, in presence or absence of candidate modulating agents.
  • Cell-protein adhesion assays measure the ability of agents to modulate the adhesion of cells to purified proteins. For example, recombinant proteins are produced, diluted to 2.5g/mL in PBS, and used to coat the wells of a microtiter plate. The wells used for negative control are not coated. Coated wells are then washed, blocked with 1% BSA, and washed again. Compounds are diluted to 2x final test concentration and added to the blocked, coated wells. Cells are then added to the wells, and the unbound cells are washed off. Retained cells are labeled directly on the plate by adding a membrane-permeable fluorescent dye, such as calcein-AM, and the signal is quantified in a fluorescent microplate reader.
  • a membrane-permeable fluorescent dye such as calcein-AM
  • Cell-cell adhesion assays measure the ability of agents to modulate binding of cell adhesion proteins with their native ligands. These assays use cells that naturally or recombinantly express the adhesion protein of choice.
  • cells expressing the cell adhesion protein are plated in wells of a multiwell plate.
  • Cells expressing the ligand are labeled with a membrane-permeable fluorescent dye, such as BCECF , and allowed to adhere to the monolayers in the presence of candidate agents. Unbound cells are washed off, and bound cells are detected using a fluorescence plate reader.
  • High-throughput cell adhesion assays have also been described.
  • small molecule ligands and peptides are bound to the surface of microscope slides using a microarray spotter, intact cells are then contacted with the slides, and unbound cells are washed off.
  • this assay not only the binding specificity of the peptides and modulators against cell lines are determined, but also the functional cell signaling of attached cells using immunofluorescence techniques in situ on the microchip is measured (Falsey JR et al., Bioconjug Chem. 2001 May-Jun;12(3):346-53).
  • An invasion/migration assay tests the ability of cells to overcome a physical barrier and to migrate towards pro-angiogenic signals.
  • Migration assays are known in the art (e.g., Paik JH et al., 2001, J Biol Chem 276:11830-11837).
  • cultured endothelial cells are seeded onto a matrix-coated porous lamina, with pore sizes generally smaller than typical cell size.
  • the matrix generally simulates the environment of the extracellular matrix, as described above.
  • the lamina is typically a membrane, such as the transwell polycarbonate membrane (Corning Costar Corporation, Cambridge, MA), and is generally part of an upper chamber that is in fluid contact with a lower chamber containing pro-angiogenic stimuli. Migration is generally assayed after an overnight incubation with stimuli, but longer or shorter time frames may also be used. Migration is assessed as the number of cells that crossed the lamina, and may be detected by staining cells with hemotoxylin solution (VWR Scientific, South San Francisco, CA), or by any other method for determining cell number. In another exemplary set up, cells are fluorescently labeled and migration is detected using fluorescent readings, for instance using the Falcon HTS FluoroBlok (Becton Dickinson).
  • a preferred assay system for migration/invasion assays comprises testing an HM's response to a variety of pro-angiogenic factors, including tumor angiogenic and inflammatory angiogenic agents, and culturing the cells in serum free medium.
  • HM-specific antibodies For antibody modulators, appropriate primary assays test is a binding assay that tests the antibody's affinity to and specificity for the HM protein. Methods for testing antibody affinity and specificity are well known in the art (Harlow and Lane, 1988, 1999, supra).
  • the enzyme-linked immunosorbant assay (ELISA) is a preferred method for detecting HM-specific antibodies; others include FACS assays, radioimmunoassays, and fluorescent assays.
  • screening assays described for small molecule modulators may also be used to test antibody modulators.
  • Primary assays for nucleic acid modulators may also be used to test antibody modulators.
  • primary assays may test the ability of the nucleic acid modulator to inhibit or enhance HM gene expression, preferably mRNA expression.
  • expression analysis comprises comparing HM expression in like populations of cells (e.g. , two pools of cells that endogenously or recombinantly express HM) in the presence and absence of the nucleic acid modulator. Methods for analyzing mRNA and protein expression are well known in the art.
  • HM mRNA expression is reduced in cells treated with the nucleic acid modulator (e.g., Current Protocols in
  • HM-modulating agents encompass candidate clinical compounds or other agents derived from previously identified modulating agent.
  • Secondary assays can also be used to test the activity of a modulating agent on a particular genetic or biochemical pathway or to test the specificity of the modulating agent's interaction with HM.
  • Secondary assays generally compare like populations of cells or animals (e.g., two pools of cells or animals that endogenously or recombinantly express HM) in the presence and absence of the candidate modulator.
  • such assays test whether treatment of cells or animals with a candidate HM-modulating agent results in changes in the p53 pathway in comparison to untreated (or mock- or placebo-treated) cells or animals.
  • Certain assays use "sensitized genetic backgrounds", which, as used herein, describe cells or animals engineered for altered expression of genes in the p53 or interacting pathways.
  • Cell based assays may use a variety of mammalian cell lines known to have defective p53 function (e.g. SAOS-2 osteoblasts, H1299 lung cancer cells, C33A andHT3 cervical cancer cells, HT-29 and DLD-1 colon cancer cells, among others, available from American Type Culture Collection (ATCC), Manassas, VA). Cell based assays may detect endogenous p53 pathway activity or may rely on recombinant expression of p53 pathway components. Any of the aforementioned assays may be used in this cell-based format.
  • Candidate modulators are typically added to the cell media but may also be injected into cells or delivered by any other efficacious means.
  • Models for defective p53 pathway typically use genetically modified animals that have been engineered to mis-express (e.g., over-express or lack expression in) genes involved in the p53 pathway. Assays generally require systemic delivery of the candidate modulators, such as by oral administration, injection, etc.
  • p53 pathway activity is assessed by monitoring neovascularization and angiogenesis.
  • Animal models with defective and normal p53 are used to test the candidate modulator's affect on HM in Matrigel® assays.
  • Matrigel® is an extract of basement membrane proteins, and is composed primarily of laminin, collagen IV, and heparin sulfate proteoglycan. It is provided as a sterile liquid at 4° C, but rapidly forms a solid gel at 37° C. Liquid Matrigel® is mixed with various angiogenic agents, such as bFGF and VEGF, or with human tumor cells which over-express .the HM.
  • mice Female athymic nude mice (Taconic, Germantown, NY) to support an intense vascular response.
  • Mice with Matrigel® pellets may be dosed via oral (PO), intraperitoneal (EP), or intravenous (IV) routes with the candidate modulator.
  • Mice are euthanized 5 - 12 days post-injection, and the Matrigel® pellet is harvested for hemoglobin analysis (Sigma plasma hemoglobin kit). Hemoglobin content of the gel is found to correlate the degree of neovascularization in the gel.
  • the effect of the candidate modulator on HM is assessed via tumorigenicity assays.
  • a xenograft comprising human cells from a pre-existing tumor or a tumor cell line is used.
  • Tumor xenograft assays are known in the art (see, e.g., Ogawa K et al, 2000, Oncogene 19:6043-6052).
  • Xenografts are typically implanted SC into female athymic mice, 6-7 week old, as single cell suspensions either from a pre-existing tumor or from in vitro culture.
  • the tumors which express the HM endogenously are injected in the flank, 1 x 10 5 to 1 x 10 cells per mouse in a volume of 100 ⁇ L using a 27 gauge needle. Mice are then ear tagged and tumors are measured twice weekly.
  • Candidate modulator treatment is initiated on the day the mean tumor weight reaches 100 mg.
  • Candidate modulator is delivered IN, SC, IP, or PO by bolus administration. Depending upon the pharmacokinetics of each unique candidate modulator, dosing can be performed multiple times per day.
  • the tumor weight is assessed by measuring perpendicular diameters with a caliper and calculated by multiplying the measurements of diameters in two dimensions.
  • the excised tumors maybe utilized for biomarker identification or further analyses.
  • xenograft tumors are fixed in 4% paraformaldehyde, 0.1M phosphate, pH 7.2, for 6 hours at 4°C, immersed in 30% sucrose in PBS, and rapidly frozen in isopentane cooled with liquid nitrogen.
  • tumorogenicity is monitored using a hollow fiber assay, which is described in U.S. Pat No. US 5,698,413.
  • the method comprises implanting into a laboratory animal a biocompatible, semi-permeable encapsulation device containing target cells, treating the laboratory animal with a candidate modulating agent, and evaluating the target cells for reaction to the candidate modulator.
  • Implanted cells are generally human cells from a pre-existing tumor or a tumor cell line. After an appropriate period of time, generally around six days, the implanted samples are harvested for evaluation of the candidate modulator.
  • Tumorogenicity and modulator efficacy may be evaluated by assaying the quantity of viable cells present in the macrocapsule, which can be determined by tests known in the art, for example, MTT dye conversion assay, neutral red dye uptake, trypan blue staining, viable cell counts, the number of colonies formed in soft agar, the capacity of the cells to recover and replicate in vitro, etc.
  • a tumorogenicity assay use a transgenic animal, usually a mouse, carrying a dominant oncogene or tumor suppressor gene knockout under the control of tissue specific regulatory sequences; these assays are generally referred to as transgenic tumor assays.
  • tumor development in the transgenic model is well characterized or is controlled.
  • the "RIPl-Tag2" transgene comprising the SV40 large T-antigen oncogene under control of the insulin gene regulatory regions is expressed in pancreatic beta cells and results in islet cell carcinomas (Hanahan D, 1985, Nature 315:115-122; Parangi S et al, 1996, Proc Natl Acad Sci USA 93: 2002-2007; Bergers G et al, 1999, Science 284:808-812).
  • the RIP1-TAG2 mice die by age 14 weeks.
  • Candidate modulators may be administered at a variety of stages, including just prior to the angiogenic switch (e.g., for a model of tumor prevention), during the growth of small tumors (e.g., for a model of intervention), or during the growth of large and/or invasive tumors (e.g., for a model of regression).
  • Tumorogenicity and modulator efficacy can be evaluating life-span extension and/or tumor characteristics, including number of tumors, tumor size, tumor morphology, vessel density, apoptotic index, etc.
  • HM-modulating agents are useful in a variety of diagnostic and therapeutic applications where disease or disease prognosis is related to defects in the p53 pathway, such as angiogenic, apoptotic, or cell proliferation disorders.
  • the invention also provides methods for modulating the p53 pathway in a cell, preferably a cell pre- determined to have defective or impaired p53 function (e.g. due to overexpression, underexpression, or misexpression of p53, or due to gene mutations), comprising the step of administering an agent to the cell that specifically modulates HM activity.
  • the modulating agent produces a detectable phenotypic change in the cell indicating that the p53 function is restored.
  • the phrase "function is restored", and equivalents, as used herein, means that the desired phenotype is achieved, or is brought closer to normal compared to untreated cells. For example, with restored p53 function, cell proliferation and/or progression through cell cycle may normalize, or be brought closer to normal relative to untreated cells.
  • the invention also provides methods for treating disorders or disease associated with impaired p53 function by administering a therapeutically effective amount of an HM -modulating agent that modulates the p53 pathway.
  • the invention further provides methods for modulating HM function in a cell, preferably a cell predetermined to have defective or impaired HM function, by administering an HM - modulating agent. Additionally, the invention provides a method for treating disorders or disease associated with impaired HM function by administering a therapeutically effective amount of an HM -modulating agent.
  • HM expression analysis methods can be used to diagnose whether HM expression occurs in a particular sample, including Northern blotting, slot blotting, ribonuclease protection, quantitative RT-PCR, and microarray analysis, (e.g., Current Protocols in Molecular Biology (1994) Ausubel FM et al, eds., John Wiley & Sons, Inc., chapter 4; Freeman WM et al, Biotechniques (1999) 26:112-125; Kallioniemi OP, Ann Med 2001, 33:142-147; Blohm and Guiseppi-Elie, Curr Opin Biotechnol 2001, 12:41-47).
  • Tissues having a disease or disorder implicating defective p53 signaling that express an HM are identified as amenable to treatment with an HM modulating agent.
  • the p53 defective tissue overexpresses an HM relative to normal tissue.
  • a Northern blot analysis of mRNA from tumor and normal cell lines, or from tumor and matching normal tissue samples from the same patient, using full or partial HM cDNA sequences as probes can determine whether particular tumors express or overexpress HM.
  • the TaqMan® is used for quantitative RT-PCR analysis of HM expression in cell lines, normal tissues and tumor samples (PE Applied Biosystems).
  • HM oligonucleotides such as the HM oligonucleotides, and antibodies directed against an HM, as described above for: (1) the detection of the presence of HM gene mutations, or the detection of either over- or under-expression of HM mRNA relative to the non-disorder state; (2) the detection of either an over- or an under-abundance of HM gene product relative to the non-disorder state; and (3) the detection of perturbations or abnormalities in the signal transduction pathway mediated by HM.
  • reagents such as the HM oligonucleotides, and antibodies directed against an HM, as described above for: (1) the detection of the presence of HM gene mutations, or the detection of either over- or under-expression of HM mRNA relative to the non-disorder state; (2) the detection of either an over- or an under-abundance of HM gene product relative to the non-disorder state; and (3) the detection of perturbations or abnormalities in the signal transduction pathway mediated by
  • the invention is drawn to a method for diagnosing a disease or disorder in a patient that is associated with alterations in HM expression, the method comprising: a) obtaining a biological sample from the patient; b) contacting the sample with a probe for HM expression; c) comparing results from step (b) with a control; and d) determining whether step (c) indicates a likelihood of the disease or disorder.
  • the disease is cancer, most preferably a cancer as shown in TABLE 2.
  • the probe may be either DNA or protein, including an antibody.
  • the Drosophila p53 gene was overexpressed specifically in the wing using the vestigial margin quadrant enhancer.
  • Increasing quantities of Drosophila p53 (titrated using different strength transgenic inserts in 1 or 2 copies) caused deterioration of normal wing morphology from mild to strong, with phenotypes including disraption of pattern and polarity of wing hairs, shortening and thickening of wing veins, progressive crumpling of the wing and appearance of dark "death" inclusions in wing blade.
  • HM name provides a symbol or the known name abbreviations for the Targets, where available, from Genbank.
  • HM RefSeq_NA or GI_NA provides the reference DNA sequences for the HMs as available from National Center for Biology Information (NCBI), HM protein Genbank identifier number (GI#), and HM description, all available from Genbank, respectively.
  • NCBI National Center for Biology Information
  • GI# HM protein Genbank identifier number
  • HM description all available from Genbank, respectively.
  • the respective SEQ ID NO for each nucleic acid and polypeptide sequence is indicated next to the sequence.
  • the length of each amino acid is in the "HM Protein Length” column.
  • Names and Protein sequences of Drosophila modifiers of p53 from screen are represented in the "Modifier Name” and “Modifier GI_AA” column by GI#, respectively.
  • HM peptide/substrate are added to each well of a 96-well microtiter plate, along with a test agent in a test buffer (10 mM HEPES, 10 mM NaCl, 6 mM magnesium chloride, pH 7.6). Changes in fluorescence polarization, determined by using a Fluorolite FPM-2 Fluorescence Polarization Microtiter System (Dynatech Laboratories, Inc), relative to control values indicates the test compound is a candidate modifier of HM activity.
  • HM peptide is added in an assay buffer (100 mM KCl, 20 mM HEPES pH 7.6, 1 mM MgCl 2 , 1% glycerol, 0.5% NP-40, 50 mM beta-mercaptoethanol, 1 mg/ml BSA, cocktail of protease inhibitors) along with a test agent to the wells of a Neutralite- avidin coated assay plate and incubated at 25°C for 1 hour. Biotinylated substrate is then added to each well and incubated for 1 hour. Reactions are stopped by washing with PBS, and counted in a scintillation counter. Test agents that cause a difference in activity relative to control without test agent are identified as candidate p53 modulating agents.
  • assay buffer 100 mM KCl, 20 mM HEPES pH 7.6, 1 mM MgCl 2 , 1% glycerol, 0.5% NP-40, 50 mM beta-mercaptoethanol, 1 mg/m
  • proteins bound to the beads are solubilized by boiling in SDS sample buffer, fractionated by SDS-polyacrylamide gel electrophoresis, transferred to polyvinylidene difluoride membrane and blotted with the indicated antibodies.
  • the reactive bands are visualized with horseradish peroxidase coupled to the appropriate secondary antibodies and the enhanced chemiluminescence (ECL) Western blotting detection system (Amersham Pharmacia Biotech).
  • CA CA
  • Taqman reactions were carried out following manufacturer's protocols, in 25 ⁇ l total volume for 96-well plates and 10 ⁇ l total volume for 384-well plates, using 300nM primer and 250 nM probe, and approximately 25ng of cDNA.
  • the standard curve for result analysis was prepared using a universal pool of human cDNA samples, which is a mixture of cDNAs from a wide variety of tissues so that the chance that a target will be present in appreciable amounts is good.
  • the raw data were normalized using 18S rRNA (universally expressed in all tissues and cells).
  • tumor tissue samples were compared with matched normal tissues from the same patient.
  • a gene was considered overexpressed in a tumor when the level of expression of the gene was 2 fold or higher in the tumor compared with its matched normal sample.
  • a universal pool of cDNA samples was used instead.
  • a gene was considered overexpressed in a tumor sample when the difference of expression levels between a tumor sample and the average of all normal samples from the same tissue type was greater than 2 times the standard deviation of all normal samples (i.e., Tumor - average(all normal samples) > 2 x STDEV(all normal samples) ).
  • Results are shown in Table 2. Number of pairs of tumor samples and matched normal tissue from the same patient are shown for each tumor type. Percentage of the samples with at least two-fold overexpression for each tumor type is provided. "ND" means not done.
  • a modulator identified by an assay described herein can be further validated for therapeutic effect by administration to a tumor in which the gene is overexpressed. A decrease in tumor growth confirms therapeutic utility of the modulator. Prior to treating a patient with the modulator, the likelihood that the patient will respond to treatment can be diagnosed by obtaining a tumor sample from the patient, and assaying for expression of the gene targeted by the modulator. The expression data for the gene(s) can also be used as a diagnostic marker for disease progression.
  • the assay can be performed by expression analysis as described above, by antibody directed to the gene target, or by any other available detection method.

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Abstract

L'invention concerne des gènes humains HM qui sont identifiés comme des modulateurs de la voie de passage de p53 et qui sont, par conséquent, des cibles thérapeutiques pour des troubles liés à une fonction déficiente de p53. L'invention concerne également des procédés d'identification de modulateurs de p53 consistant à rechercher des agents modulateurs de l'activité de HM.
PCT/US2002/033542 2001-10-22 2002-10-21 Modificateurs de la voie de passage de p53 et leurs procedes d'utilisation WO2003035833A2 (fr)

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US8932821B2 (en) 2003-03-19 2015-01-13 Biogen Idec Ma Inc. NOGO receptor binding protein
US8765662B2 (en) 2003-03-19 2014-07-01 Biogen Idec Ma Inc. NOGO receptor binding protein
EP2182006A3 (fr) * 2003-08-11 2010-09-15 Genentech, Inc. Compositions et procédés pour le traitement de maladies liées au système immunitaire
EP2014675A1 (fr) * 2003-08-11 2009-01-14 Genentech, Inc. Compositions et procédés pour le traitement de maladies liées au système immunitaire
EP2182006A2 (fr) * 2003-08-11 2010-05-05 Genentech, Inc. Compositions et procédés pour le traitement de maladies liées au système immunitaire
US8486893B2 (en) 2004-06-24 2013-07-16 Biogen Idec Ma Inc. Treatment of conditions involving demyelination
US9068992B2 (en) 2004-06-24 2015-06-30 Biogen Ma Inc. Screening methods for identifying Sp35 antagonists
WO2006111946A2 (fr) * 2005-04-18 2006-10-26 The Provost, Fellows And Scholars Of The College Of The Holy And Undivided Trinity Of Queen Elizabeth, Near Dublin Polypeptides et utilisation de ceux-ci
WO2006111946A3 (fr) * 2005-04-18 2007-03-01 Trinity College Dublin Polypeptides et utilisation de ceux-ci
JP2012121888A (ja) * 2005-04-18 2012-06-28 Provost Fellows & Scholars Of The College Of The Holy & Undivided Trinity Of Queen Elizabeth Near Dublin トール様レセプター１４（ｔｌｒ１４）及びそれらの使用
AU2006238475B2 (en) * 2005-04-18 2012-09-27 Opsona Therapeutics Limited Toll-like receptor 14 (TLR14 ) and use thereof
JP2008538498A (ja) * 2005-04-18 2008-10-30 ザ・プロヴォスト，フェローズ・アンド・スカラーズ・オブ・ザ・カレッジ・オブ・ザ・ホーリー・アンド・アンディヴァイデッド・トリニティー・オブ・クイーン・エリザベス，ニア・ダブリン トール様レセプター１４（ｔｌｒ１４）及びそれらの使用
US9066984B2 (en) 2005-07-08 2015-06-30 Biogen Ma Inc. Sp35 antibodies and uses thereof
US8551476B2 (en) 2005-07-08 2013-10-08 Biogen Idec Ma Inc. SP35 antibodies and uses thereof
US8414887B2 (en) 2006-10-18 2013-04-09 Opsona Therapeutics Limited Methods for suppressing Toll-like Receptor 4 (TLR4) function using TLR14 antagonists
US20100297147A1 (en) * 2006-10-18 2010-11-25 Wyeth Compositions and methods for modulating tlr14 activity
US8609407B2 (en) 2007-01-09 2013-12-17 Biogen Idec Ma Inc. Sp35 antibodies and uses thereof
US8128926B2 (en) 2007-01-09 2012-03-06 Biogen Idec Ma Inc. Sp35 antibodies and uses thereof
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US8058406B2 (en) 2008-07-09 2011-11-15 Biogen Idec Ma Inc. Composition comprising antibodies to LINGO or fragments thereof
US9745375B2 (en) 2008-07-09 2017-08-29 Biogen Ma Inc. Compositions comprising antibodies to LINGO or fragments thereof
US9994646B2 (en) 2009-09-16 2018-06-12 Genentech, Inc. Coiled coil and/or tether containing protein complexes and uses thereof
US9796780B2 (en) 2012-05-14 2017-10-24 Biogen Ma Inc. LINGO-2 antagonists for treatment of conditions involving motor neurons
US10435467B2 (en) 2015-01-08 2019-10-08 Biogen Ma Inc. LINGO-1 antagonists and uses for treatment of demyelinating disorders

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