WO2003074663A2 - Genes mp21 utilises comme modificateurs de la voie p21 et procedes d'utilisation correspondants - Google Patents

Genes mp21 utilises comme modificateurs de la voie p21 et procedes d'utilisation correspondants Download PDF

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WO2003074663A2
WO2003074663A2 PCT/US2003/006088 US0306088W WO03074663A2 WO 2003074663 A2 WO2003074663 A2 WO 2003074663A2 US 0306088 W US0306088 W US 0306088W WO 03074663 A2 WO03074663 A2 WO 03074663A2
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assay
agent
cell
candidate
assay system
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Marcia Belvin
Lori Friedman
Gregory D. Plowman
Timothy S. Heuer
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Exelixis, Inc.
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4702—Regulators; Modulating activity

Definitions

  • the p21/CDKNl/WAFl/CIPl protein (El-Deiry, W. S.; et al. Cell 75: 817-825, 1993; Harper, J. W.; et al. Cell 75: 805-816, 1993; Huppi, Ket al. Oncogene 9: 3017-3020, 1994) is a cell cycle control protein that inhibits cyclin-kinase activity, is tightly regulated at the transcriptional level by p21, and mediates p21 suppression of tumor cell growth. Along with p21, p21 appears to be essential for maintaining the G2 checkpoint in human cells (Bunz, F.; Dutriaux, A.; et al. Science 282:1497-1501, 1998).
  • Sequences of P21 are well-conserved throughout evolution, and have been identified in species as diverse as human (Genbank Identifier 13643057), Drosophila melanogaster (GI# 1684911), Caenorhabditis elegans (GI#4966283), and yeast (GI#2656016).
  • NR5A1 (Oba et al., (1996) Biochem. Biophys. Res. Commun. 226: 261-267), also known as SFl or FTZl, is closely related to an orphan nuclear receptor isolated from Drosophila, designated fushi tarazu factor-1, or FTZ-F1 (Lala et al, (1992) Molec. Endocr. 6: 1249-1258), which plays an important role in Drosophila development.
  • NR5A is implicated in the gene regulation of at least 3 enzymes required for the biosynthesis of corticosteroids, and plays crucial roles in the process of nonsteroidogenic as well as steroidogenic tissue differentiation, and thus, contributes to tissue development from the earliest stages of ontogeny (Morohashi K. (1999) Trends Endocr. Metab. 10: 169-173).
  • NR5A2 (Li et al (1998) J Biol. Chem. 273: 29022-29031), also known as FTF, HB1F, or CPF, also belongs to the fushi tarazu factor- 1 (FTZ-F1) subfamily of orphan nuclear receptors and is closely related to NR5A1.
  • NR5A2 is a key regulator of human CYP7A gene expression in the liver (Nitta, M et al. (1999) Proc. Nat. Acad. Sci. 96: 6660-6665). CYP7A is an enzyme expressed exclusively in the liver, and plays a central role in cholesterol homeostasis.
  • NR6A1 (Agoulnik et al (1998) FEBS Lett. 424: 73-78), also known as GCNF or RTR, is another member of the FTZ-F1 family, is expressed at high levels only in the testis, with expression restricted to germ cells, the spermatids and late-stage spermatocytes.
  • the DAZ (for 'deleted in azoospermia') gene is transcribed in the adult testis and appears to encode an RNA-binding protein.
  • the DAZ gene product may play a role in the germ-cell-specific patterns of RNA splicing and storage. (Cooke, H. J, et al., (1996) Hum. Molec. Genet. 5: 513-516). Deletions encompassing the Y chromosomal DAZ genes are the most common molecularly defined cause of infertility in humans.
  • DAZ homologs An array of 4 DAZ genes in 2 clusters is located on the Y chromosome and encodes RNA-binding proteins with a common RNA recognition motif and a series of 8 to 18 DAZ repeats consisting of 24 amino acids each that are rich in N, Y, and Q amino acid residues.
  • DAZ homologs identified in diverse organisms, are required for germ cell development but differ in null phenotypes and expression patterns. In flies, disruption of the DAZ homolog 'Boule' causes male meiotic arrest (Eberhart et al., (1996) Nature 381: 783-785).
  • the human and mouse BOULE resemble the invertebrate meiotic regulator Boule, the proposed ortholog of DAZ, in sequence and expression pattern, and hence likely perform a similar meiotic function.
  • human DAZ and DAZL are expressed much earlier than BOULE in prenatal germ stem cells and spermatogonia; DAZL also is expressed in female germ cells.
  • homologs of the DAZ gene family can be grouped into 2 subfamilies (BOULE and DAZL) and further, members of the DAZ family evolved from an ancestral meiotic regulator, Boule, to assume distinct, yet overlapping, functions in germ cell development (Xu, E. et al., (2001) Proc. Nat. Acad. Sci. 98: 7414-7419).
  • model organisms such as Drosophila
  • Drosophila 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. Due to a high level of gene and pathway conservation, the strong similarity of cellular processes, and the functional conservation of genes between these model organisms and mammals, identification of the involvement of novel genes in particular pathways and their functions in such model organisms can directly contribute to the understanding of the correlative pathways and methods of modulating them in mammals (see, for example, Mechler BM et al., 1985 EMBO J 4:1551-1557; Gateff E. 1982 Adv. Cancer Res. 37: 33- 74; Watson KL., et al., 1994 J Cell Sci.
  • 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.
  • the gene When 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.
  • the genetic entry point is an ortholog of a human gene implicated in a disease pathway, such as p21, modifier genes can be identified that may be attractive candidate targets for novel therapeutics.
  • MP21 modify the p21 pathway in Drosophila, and identified their human orthologs, hereinafter referred to as modifiers of p21 (MP21).
  • the invention provides methods for utilizing these p21 modifier genes and polypeptides to identify MP21 -modulating agents that are candidate therapeutic agents that can be used in the treatment of disorders associated with defective or impaired p21 function and/or MP21 function.
  • Preferred MP21 -modulating agents specifically bind to MP21 polypeptides and restore p21 function.
  • Other preferred MP21 -modulating agents are nucleic acid modulators such as antisense oligomers and RNAi that repress MP21 gene expression or product activity by, for example, binding to and inhibiting the respective nucleic acid (i.e. DNA or mRNA).
  • MP21 modulating agents may be evaluated by any convenient in vitro or in vivo assay for molecular interaction with an MP21 polypeptide or nucleic acid.
  • candidate MP21 modulating agents are tested with an assay system comprising a MP21 polypeptide or nucleic acid.
  • Agents that produce a change in the activity of the assay system relative to controls are identified as candidate p21 modulating agents.
  • the assay system may be cell-based or cell-free.
  • MP21 -modulating agents include MP21 related proteins (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 p21 pathway modulating agents are further tested using a second assay system that detects changes in the p21 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 p21 pathway, such as an angiogenic, apoptotic, or cell proliferation disorder (e.g. cancer).
  • the invention further provides methods for modulating the MP21 function and/or the p21 pathway in a mammalian cell by contacting the mammalian cell with an agent that specifically binds a MP21 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 p21 pathway.
  • MP21 modulating agents that act by inhibiting or enhancing MP21 expression, directly or indirectly, for example, by affecting an MP21 function such as binding activity, can be identified using methods provided herein.
  • MP21 modulating agents are useful in diagnosis, therapy and pharmaceutical development.
  • Genbank referenced by Genbank identifier (GI) number
  • Genbank identifier GI#s 4826731 (SEQ ID NO:l)
  • 4504342 SEQ ID NO:2
  • 15451847 SEQ ID NO:3
  • 14719413 SEQ ID NO:4
  • 6552325 SEQ ID NO:5
  • MP21 polypeptide refers to a full-length MP21 protein or a functionally active fragment or derivative thereof.
  • a "functionally active" MP21 fragment or derivative exhibits one or more functional activities associated with a full-length, wild- type MP21 protein, such as anti genie or immunogenic activity, ability to bind natural cellular substrates, etc.
  • the functional activity of MP21 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 MP21 polypeptide is a MP21 derivative capable of rescuing defective endogenous MP21 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 MP21, 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). For example, the RNA recognition domain of MP21 from GI# 14719414 (SEQ ID NO:9) is located at approximately amino acid residues 35-105 (PFAM 00076).
  • 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:6-10 (an MP21).
  • the fragment comprises the entire functionally active domain.
  • MP21 nucleic acid refers to a DNA or RNA molecule that encodes a MP21 polypeptide.
  • the MP21 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 MP21.
  • 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.
  • nucleic acid molecules of the subject nucleic acid molecules include sequences that hybridize to the nucleic acid sequence of any ofSEQ ID NOs:l-5.
  • 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.
  • 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-5 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 are used that are: pretreatment of filters containing nucleic acid for 6 h at 40° C in a solution containing 35% formamide, 5X SSC, 50 mM Tris-HCl (pH7.5), 5mM EDTA, 0.1% PNP, 0.1% Ficoll, 1% BSA, and 500 ⁇ g/ml denatured salmon sperm D ⁇ A; hybridization for 18-20h at 40° C in a solution containing 35% formamide, 5X SSC, 50 mM Tris-HCl ( ⁇ H7.5), 5mM EDTA, 0.02% PNP, 0.02% Ficoll, 0.2% BSA, 100 ⁇ g/ml salmon sperm D ⁇ A, 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 are: 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 D ⁇ A; 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.
  • MP21 nucleic acids and polypeptides useful for identifying and testing agents that modulate MP21 function and for other applications related to the involvement of MP21 in the p21 pathway.
  • MP21 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.
  • Proteins to be purified for screening or antibody production may require the addition of specific tags (e.g., generation of fusion proteins).
  • Overexpression of an MP21 protein for assays used to assess MP21 function, such as involvement in cell cycle regulation or hypoxic response, may require expression in eukaryotic cell lines capable of these cellular activities.
  • recombinant MP21 is expressed in a cell line known to have defective p21 function such as HCT116 colon cancer cells available from American Type Culture Collection (ATCC), Manassas, VA).
  • ATCC American Type Culture Collection
  • VA Manassas
  • the recombinant cells are used in cell-based screening assay systems of the invention, as described further below.
  • the nucleotide sequence encoding an MP21 polypeptide can be inserted into any appropriate expression vector.
  • the necessary transcriptional and translational signals, including promoter/enhancer element can derive from the native MP21 gene and/or 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.
  • the expression vector can comprise a promoter operably linked to an MP21 gene nucleic acid, one or more origins of replication, and, one or more selectable markers (e.g. thymidine kinase activity, resistance to antibiotics, etc.).
  • recombinant expression vectors can be identified by assaying for the expression of the MP21 gene product based on the physical or functional properties of the MP21 protein in in vitro assay systems (e.g. immunoassays).
  • the MP21 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 MP21 proteins can be purified from natural sources, by standard methods (e.g. immunoaffinity purification). 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.
  • the methods of this invention may also use cells that have been engineered for altered expression (mis-expression) of MP21 or other genes associated with the p21 pathway.
  • 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 MP21 expression may be used in in vivo assays to test for activity of a candidate p21 modulating agent, or to further assess the role of MP21 in a p21 pathway process such as apoptosis or cell proliferation.
  • the altered MP21 expression results in a detectable phenotype, such as decreased or increased levels of cell proliferation, angiogenesis, or apoptosis compared to control animals having normal MP21 expression.
  • the genetically modified animal may additionally have altered p21 expression (e.g. p21 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 extrachromosomal 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. Methods of making transgenic animals are well-known in the art (for transgenic mice see Brinster et al., Proc. Nat.
  • the transgenic animal is a "knock-out" animal having a heterozygous or homozygous alteration in the sequence of an endogenous MP21 gene that results in a decrease of MP21 function, preferably such that MP21 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 MP21 gene is used to construct a homologous recombination vector suitable for altering an endogenous MP21 gene in the mouse genome.
  • Detailed methodologies for homologous recombination in mice are available (see Capecchi, Science (1989) 244: 1288-1292; Joyner et al, Nature (1989)
  • 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 MP21 gene, e.g., by introduction of additional copies of MP21, or by operatively inserting a regulatory sequence that provides for altered expression of an endogenous copy of the MP21 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 p21 pathway, as animal models of disease and disorders implicating defective p21 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 MP21 function and phenotypic changes are compared with appropriate control animals such as genetically modified animals that receive placebo treatment, and/or animals with unaltered MP21 expression that receive candidate therapeutic agent.
  • animal models having defective p21 function can be used in the methods of the present invention.
  • a p21 knockout mouse can be used to assess, in vivo, the activity of a candidate p21 modulating agent identified in one of the in vitro assays described below.
  • p21 knockout mice are described in the literature (Umanoff H, et al., Proc Natl Acad Sci U S A 1995 Feb 28;92(5): 1709-13).
  • the candidate p21 modulating agent when administered to a model system with cells defective in p21 function, produces a detectable phenotypic change in the model system indicating that the p21 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 MP21 and or the p21 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 p21 pathway, as well as in further analysis of the MP21 protein and its contribution to the p21 pathway.
  • the invention also provides methods for modulating the p21 pathway comprising the step of specifically modulating MP21 activity by administering a MP21- interacting or -modulating agent.
  • an "MP21 -modulating agent” is any agent that modulates MP21 function, for example, an agent that interacts with MP21 to inhibit or enhance MP21 activity or otherwise affect normal MP21 function.
  • MP21 function can be affected at any level, including transcription, protein expression, protein localization, and cellular or extra-cellular activity.
  • the MP21 - modulating agent specifically modulates the function of the MP21.
  • the phrases "specific modulating agent”, “specifically modulates”, etc., are used herein to refer to modulating agents that directly bind to the MP21 polypeptide or nucleic acid, and preferably inhibit, enhance, or otherwise alter, the function of the MP21.
  • the MP21- modulating agent is a modulator of the p21 pathway (e.g. it restores and/or upregulates p21 function) and thus is also a p21 -modulating agent.
  • Preferred MP21 -modulating agents include small molecule compounds; MP21- 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 MP21 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 MP21-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 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 p21 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.
  • MP21-interacting proteins are useful in a variety of diagnostic and therapeutic applications related to the p21 pathway and related disorders, as well as in validation assays for other MP21 -modulating agents.
  • MP21- interacting proteins affect normal MP21 function, including transcription, protein expression, protein localization, and cellular or extra-cellular activity.
  • MP21 -interacting proteins are useful in detecting and providing information about the function of MP21 proteins, as is relevant to p21 related disorders, such as cancer (e.g., for diagnostic means).
  • An MP21 -interacting protein may be endogenous, i.e. one that naturally interacts genetically or biochemically with an MP21, such as a member of the MP21 pathway that modulates MP21 expression, localization, and/or activity.
  • MP21 -modulators include dominant negative forms of MP21 -interacting proteins and of MP21 proteins themselves.
  • Yeast two-hybrid and variant screens offer preferred methods for identifying endogenous MP21 -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.
  • 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 MP21 -interacting protein may be an exogenous protein, such as an MP21-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). MP21 antibodies are further discussed below.
  • an MP21 -interacting protein specifically binds an MP21 protein.
  • an MP21 -modulating agent binds an MP21 substrate, binding partner, or cofactor.
  • the protein modulator is an MP21 specific antibody agonist or antagonist.
  • the antibodies have therapeutic and diagnostic utilities, and can be used in screening assays to identify MP21 modulators.
  • the antibodies can also be used in dissecting the portions of the MP21 pathway responsible for various cellular responses and in the general processing and maturation of the MP21.
  • Antibodies that specifically bind MP21 polypeptides can be generated using known methods.
  • the antibody is specific to a mammalian ortholog of MP21 polypeptide, and more preferably, to human MP21.
  • 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.
  • Epitopes of MP21 which are particularly antigenic can be selected, for example, by routine screening of MP21 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:6- 10.
  • Monoclonal antibodies with affinities of 10 8 M “1 preferably 10 9 M “1 to 10 10 M “1 , or stronger can be made by standard procedures as described (Harlow and Lane, supra; Goding (1986) Monoclonal Antibodies: Principles and Practice (2d ed) Academic Press, New York; and U.S. Pat. Nos. 4,381,292; 4,451,570; and 4,618,577).
  • Antibodies may be generated against crude cell extracts of MP21 or substantially purified fragments thereof. If MP21 fragments are used, they preferably comprise at least 10, and more preferably, at least 20 contiguous amino acids of an MP21 protein.
  • MP21- 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.
  • the presence of MP21 -specific antibodies is assayed by an appropriate assay such as a solid phase enzyme-linked immunosorbant assay (ELISA) using immobilized corresponding MP21 polypeptides.
  • ELISA solid phase enzyme-linked immunosorbant assay
  • Other assays such as radioimmunoassays or fluorescent assays might also be used.
  • Chimeric antibodies specific to MP21 polypeptides can be made that contain different portions from different animal species.
  • 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. Natl. Acad. Sci. (1984) 81:6851-6855; Neuberger et al., Nature (1984) 312:604-608; Takeda et al., Nature (1985) 31:452-454).
  • 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 Nature 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).
  • MP21 -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. 3,817,837; 3,850,752; 3,939,350;
  • 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 e.g., 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 about 10 mg/ml. Immunotherapeutic methods are further described in the literature (US Pat. No. 5,859,206; WO0073469).
  • MP21 -modulating agents comprise nucleic acid molecules, such as antisense oligomers or double stranded RNA (dsRNA), which generally inhibit MP21 activity.
  • Preferred nucleic acid modulators interfere with the function of the MP21 nucleic acid such as DNA replication, transcription, translocation of the MP21 RNA to the site of protein translation, translation of protein from the MP21 RNA, splicing of the MP21 RNA to yield one or more mRNA species, or catalytic activity which may be engaged in or facilitated by the MP21 RNA.
  • the antisense oligomer is an oligonucleotide that is sufficiently complementary to an MP21 mRNA to bind to and prevent translation, preferably by binding to the 5' untranslated region.
  • MP21-specific antisense oligonucleotides preferably range from at least 6 to about 200 nucleotides. In some embodiments the oligonucleotide is preferably at least 10, 15, or 20 nucleotides in length. In other embodiments, 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 Oligodeoxynucleotide and Ribozyme Design, Methods. (2000) 22(3):271-281; Summerton J, and Weller D. 1997 Antisense Nucleic Acid Drug Dev. :7: 187-95; US Pat. No. 5,235,033; and US Pat No. 5,378,841).
  • 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 extraordinar 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. For example, 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.
  • an MP21 -specific nucleic acid modulator is used in an assay to further elucidate the role of the MP21 in the p21 pathway, and/or its relationship to other members of the pathway.
  • an MP21-specific antisense oligomer is used as a therapeutic agent for treatment of p21- 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 MP21 nucleic acid or protein.
  • secondary assays further assess the activity of a MP21 modulating agent identified by a primary assay and may confirm that the modulating agent affects MP21 in a manner relevant to the p21 pathway. In some cases, MP21 modulators will be directly tested in a secondary assay.
  • the screening method comprises contacting a suitable assay system comprising an MP21 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 MP21 activity, and hence the p21 pathway.
  • the MP21 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.
  • Cell-based screening assays usually require systems for recombinant expression of MP21 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. In certain applications, when MP21 -interacting proteins are used in screens to identify small molecule modulators, the binding specificity of the interacting protein to the MP21 protein may be assayed by various known methods such as substrate processing (e.g.
  • binding equilibrium constants usually at least about 10 7 M "1 , preferably at least about 10 8 M "1 , more preferably at least about 10 9 M " *
  • immunogenicity e.g. ability to elicit MP21 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 a MP21 polypeptide, a fusion protein thereof, or to cells or membranes bearing the polypeptide or fusion protein.
  • the MP21 polypeptide can be full length or a fragment thereof that retains functional MP21 activity.
  • the MP21 polypeptide may be fused to another polypeptide, such as a peptide tag for detection or anchoring, or to another tag.
  • the MP21 polypeptide is preferably human MP21, or is an ortholog or derivative thereof as described above.
  • the screening assay detects candidate agent-based modulation of MP21 interaction with a binding target, such as an endogenous or exogenous protein or other substrate that has MP21 -specific binding activity, and can be used to assess normal MP21 gene function.
  • a binding target such as an endogenous or exogenous protein or other substrate that has MP21 -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.
  • a variety of suitable assay systems may be used to identify candidate MP21 and p21 pathway modulators (e.g. U.S. Pat. Nos. 5,550,019 and 6,133,437 (apoptosis assays); and U.S. Pat. Nos. 5,976,782, 6,225,118 and 6,444,434 (angiogenesis assays), among others). Specific preferred assays are described in more detail below.
  • RNA is associated with RNA-binding proteins (RBPs) that protect, stabilize, package or transport RNA, mediate RNA interactions with other biomolecules or act catalytically on RNA.
  • RBPs RNA-binding proteins
  • the structural information obtained for RNA alone and RNA-protein complexes has elucidated a variety of RNA tertiary structures and diverse modes for RNA-protein interaction.
  • the specific interaction of proteins with highly structured RNAs makes it possible to target unique RNA motifs with small molecules, thus making RNA an interesting target for therapeutic intervention.
  • Assays for RNA binding or processing may be based on homogeneous scintillation proximity (Liu J, et al., Anal Biochem 2001 289:239-245), chemiluminescense (Mazumder A, Nucleic Acids Res 1998 26:1996-2000), gel shift (Stull RA, et al., Antisense Nucleic Acid Drug Dev 1996 6:221-228; U.S. Pat. No: 6004749).
  • Nuclear receptors are a superf amily of ligand-dependent transcription factors that mediate the effects of hormones and other endogenous ligands to regulate the expression of specific genes.
  • High throughput assays for nuclear receptors include fluorescent polarization binding assays (Lin S, et al. (2002) Anal Biochem 300(1): 15-21), and homogeneous time-resolved fluorescence energy transfer (Zhou G, et al. (2001) Methods 25:54-61), among others.
  • 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 MP21, and that optionally has defective p21 function (e.g. p21 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 p21 modulating agents.
  • an apoptosis assay may be used as a secondary assay to test a candidate p21 modulating agents that is initially identified using a cell-free assay system.
  • An apoptosis assay may also be used to test whether MP21 function plays a direct role in apoptosis.
  • an apoptosis assay may be performed on cells that over- or under-express MP21 relative to wild type cells. Differences in apoptotic response compared to wild type cells suggests that the MP21 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 incorporation 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 et al, 1988, J. Immunol. Meth. 107, 79), or by other means.
  • Cell Proliferation may also be examined using [ 3 H]-thymidine incorporation (Chen, J., 1996, Oncogene 13:1395-403; Jeoung, J., 1995, J. Biol. Chem. 270:18367-73).
  • This assay allows for quantitative characterization of S-phase DNA syntheses.
  • cells synthesizing DNA will incorporate [ 3 H]-thymidine into newly synthesized DNA. Incorporation can then be measured by standard techniques such as by counting of radioisotope in a scintillation counter (e.g., Beckman LS 3800 Liquid Scintillation Counter).
  • 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 (Noytik-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 MP21 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 MP21 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 MP21, and that optionally has defective p21 function (e.g. p21 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 p21 modulating agents.
  • the cell proliferation or cell cycle assay may be used as a secondary assay to test a candidate p21 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 MP21 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 MP21 relative to wild type cells. Differences in proliferation or cell cycle compared to wild type cells suggests that the MP21 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 MP21, and that optionally has defective p21 function ' (e.g. p21 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 p21 modulating agents.
  • the angiogenesis assay may be used as a secondary assay to test a candidate p21 modulating agents that is initially identified using another assay system.
  • An angiogenesis assay may also be used to test whether MP21 function plays a direct role in cell proliferation.
  • an angiogenesis assay may be performed on cells that over- or under-express MP21 relative to wild type cells. Differences in angiogenesis compared to wild type cells suggests that the MP21 plays a direct role in angiogenesis.
  • hypoxia inducible factor-1 The alpha subunit of the transcription factor, hypoxia inducible factor-1 (HIF-1), is upregulated in tumor cells following exposure to hypoxia in vitro.
  • HIF-1 hypoxia inducible factor-1
  • hypoxia inducible factor-1 stimulates the expression of genes known to be important in tumour cell survival, such as those encoding glyolytic enzymes and NEGF.
  • Induction of such genes by hypoxic conditions may be assayed by growing cells transfected with MP21 in hypoxic conditions (such as with 0.1% 02, 5% CO2, and balance ⁇ 2, 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 MP21, and that optionally has defective p21 function (e.g. p21 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 p21 modulating agents.
  • the hypoxic induction assay may be used as a secondary assay to test a candidate p21 modulating agents that is initially identified using another assay system.
  • a hypoxic induction assay may also be used to test whether MP21 function plays a direct role in the hypoxic response.
  • a hypoxic induction assay may be performed on cells that over- or under-express MP21 relative to wild type cells. Differences in hypoxic response compared to wild type cells suggests that the MP21 plays a direct role in hypoxic induction.
  • Cell adhesion measures 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. Httgh-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).
  • Tubulogenesis assays monitor the ability of cultured cells, generally endothelial cells, to form tubular structures on a matrix substrate, which generally simulates the environment of the extracellular matrix.
  • exemplary substrates include MatrigelTM (Becton Dickinson), an extract of basement membrane proteins containing laminin, collagen IN, and heparin sulfate proteoglycan, which is liquid at 4° C and forms a solid gel at 37° C.
  • Other suitable matrices comprise extracellular components such as collagen, fibronectin, and/or fibrin. Cells are stimulated with a pro-angiogenic stimulant, and their ability to form tubules is detected by imaging.
  • Tubules can generally be detected after an overnight incubation with stimuli, but longer or shorter time frames may also be used.
  • Tube formation assays are well known in the art (e.g., Jones MK et al., 1999, Nature Medicine 5:1418-1423). These assays have traditionally involved stimulation with serum or with the growth factors FGF or VEGF. Serum represents an undefined source of growth factors.
  • the assay is performed with cells cultured in serum free medium, in order to control which process or pathway a candidate agent modulates.
  • different target genes respond differently to stimulation with different pro-angiogenic agents, including inflammatory angiogenic factors such as TNF-alpa.
  • a tubulogenesis assay system comprises testing an MP21's response to a variety of factors, such as FGF, VEGF, phorbol myristate acetate (PMA), TNF-alpha, ephrin, etc.
  • factors such as FGF, VEGF, phorbol myristate acetate (PMA), TNF-alpha, ephrin, etc.
  • 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 MP21's response to a variety of pro-angiogenic factors, including tumor angiogenic and inflammatory angiogenic agents, and culturing the cells in serum free medium.
  • a sprouting assay is a three-dimensional in vitro angiogenesis assay that uses a cell-number defined spheroid aggregation of endothelial cells ("spheroid"), embedded in a collagen gel-based matrix.
  • the spheroid can serve as a starting point for the sprouting of capillary-like structures by invasion into the extracellular matrix (termed “cell sprouting") and the subsequent formation of complex anastomosing networks (Korff and Augustin, 1999, J Cell Sci 112:3249-58).
  • cell sprouting the extracellular matrix
  • spheroids are prepared by pipetting 400 human umbilical vein endothelial cells into individual wells of a nonadhesive 96-well plates to allow overnight spheroidal aggregation (Korff and Augustin: J Cell Biol 143: 1341-52, 1998).
  • Spheroids are harvested and seeded in 900 ⁇ l of methocel-collagen solution and pipetted into individual wells of a 24 well plate to allow collagen gel polymerization. Test agents are added after 30 min by pipetting 100 ⁇ l of 10-fold concentrated working dilution of the test substances on top of the gel. Plates are incubated at 37°C for 24h. Dishes are fixed at the end of the experimental incubation period by addition of paraformaldehyde. Sprouting intensity of endothelial cells can be quantitated by an automated image analysis system to determine the cumulative sprout length per spheroid.
  • ELISA enzyme-linked immunosorbant assay
  • primary assays may test the ability of the nucleic acid modulator to inhibit or enhance MP21 gene expression, preferably mRNA expression.
  • expression analysis comprises comparing MP21 expression in like populations of cells (e.g., two pools of cells that endogenously or recombinantly express MP21) in the presence and absence of the nucleic acid modulator. Methods for analyzing mRNA and protein expression are well known in the art.
  • Protein expression may also be monitored. Proteins are most commonly detected with specific antibodies or antisera directed against either the MP21 protein or specific peptides. A variety of means including Western blotting, ELISA, or in situ detection, are available (Harlow E and Lane D, 1988 and 1999, supra).
  • screening assays described for small molecule modulators may also be used to test nucleic acid modulators.
  • Secondary assays may be used to further assess the activity of MP21 -modulating agent identified by any of the above methods to confirm that the modulating agent affects MP21 in a manner relevant to the p21 pathway.
  • MP21 -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 MP21.
  • Secondary assays generally compare like populations of cells or animals (e.g., two pools of cells or animals that endogenously or recombinantly express MP21) in the presence and absence of the candidate modulator. In general, such assays test whether treatment of cells or animals with a candidate MP21-modulating agent results in changes in the p21 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 p21 or interacting pathways.
  • Cell based assays may use a variety of mammalian cell lines known to have defective p21 function such as HCT116 colon cancer cells available from American Type Culture Collection (ATCC), Manassas, VA). Cell based assays may detect endogenous p21 pathway activity or may rely on recombinant expression of p21 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 p21 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 p21 pathway.
  • Assays generally require systemic delivery of the candidate modulators, such as by oral administration, injection, etc.
  • p21 pathway activity is assessed by monitoring neovascularization and angiogenesis.
  • Animal models with defective and normal p21 are used to test the candidate modulator's affect on MP21 in Matrigel® assays.
  • Matrigel® is an extract of basement membrane proteins, and is composed primarily of laminin, collagen IN, 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 NEGF, or with human tumor cells which over-express the MP21.
  • mice Female athymic nude mice (Taconic, Germantown, ⁇ Y) to support an intense vascular response.
  • Mice with Matrigel® pellets may be dosed via oral (PO), intraperitoneal (IP), or intravenous (IN) 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 MP21 is assessed via tumorigenicity assays.
  • 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 preexisting tumor or from in vitro culture. The tumors which express the MP21 endogenously are injected in the flank, 1 x 10 5 to 1 x 10 7 cells per mouse in a volume of 100 ⁇ L using a 27gauge 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.
  • 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 SN40 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.
  • MP21 -modulating agents are useful in a variety of diagnostic and therapeutic applications where disease or disease prognosis is related to defects in the p21 pathway, such as angiogenic, apoptotic, or cell proliferation disorders.
  • the invention also provides methods for modulating the p21 pathway in a cell, preferably a cell pre-determined to have defective or impaired p21 function (e.g. due to overexpression, underexpression, or misexpression of p21, or due to gene mutations), comprising the step of administering an agent to the cell that specifically modulates MP21 activity.
  • the modulating agent produces a detectable phenotypic change in the cell indicating that the p21 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 p21 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 p21 function by administering a therapeutically effective amount of an MP21 -modulating agent that modulates the p21 pathway.
  • the invention further provides methods for modulating MP21 function in a cell, preferably a cell pre-determined to have defective or impaired MP21 function, by administering an MP21 -modulating agent. Additionally, the invention provides a method for treating disorders or disease associated with impaired MP21 function by administering a therapeutically effective amount of an MP21 -modulating agent.
  • Various expression analysis methods can be used to diagnose whether MP21 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 p21 signaling that express an MP21 are identified as amenable to treatment with an MP21 modulating agent.
  • the p21 defective tissue overexpresses an MP21 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 MP21 cDNA sequences as probes can determine whether particular tumors express or overexpress MP21.
  • the TaqMan® is used for quantitative RT-PCR analysis of MP21 expression in cell lines, normal tissues and tumor samples (PE Applied Biosystems).
  • reagents such as the MP21 oligonucleotides, and antibodies directed against an MP21, as described above for: (1) the detection of the presence of MP21 gene mutations, or the detection of either over- or under-expression of MP21 mRNA relative to the non-disorder state; (2) the detection of either an over- or an under-abundance of MP21 gene product relative to the non-disorder state; and (3) the detection of perturbations or abnormalities in the signal transduction pathway mediated by MP21.
  • the invention is drawn to a method for diagnosing a disease or disorder in a patient that is associated with alterations in MP21 expression, the method comprising: a) obtaining a biological sample from the patient; b) contacting the sample with a probe for MP21 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 1.
  • the probe may be either DNA or protein, including an antibody.
  • Drosophila p21 screen An overexpression screen was carried out in Drosophila to identify genes that interact with the cyclin dependent kinase inhibitor, p21 (Bourne HR, et al., Nature (1990) 348(6297): 125-132; Marshall CJ, Trends Genet (1991) 7(3):91-95). Expression of the p21 gene in the eye causes deterioration of normal eye morphology. Modifiers of the eye phenotype were identified as members of the p21 pathway. CG8676 and CG4760 were suppressors of the wing phenotype. Human orthologs of the modifiers are referred to herein as MP21. BLAST analysis (Altschul et al., supra) was employed to identify orthologs of
  • Drosophila modifiers For example, representative sequences from MP21, GI# 4826732 (SEQ ID NO:6), GI#4504343 (SEQ ID NO:7), and GI# 15451848 (SEQ ID NO:8) share 30%, 31%, and 30% amino acid identity, respectively, with the Drosophila CG8676. Likewise, GI# 14719414 (SEQ ID NO:9) and GI#4758122 (SEQ ID NO: 10) share 50% and 44% amino acid identity, respectively, with the Drosophila CG4760.
  • GI#s 4826732, 4504343, and 15451848 (SEQ ID Nos: 6, 7, and 8, respectively), each have a C4 type zinc finger domain (PFAM00105), located approximately at amino acid residues 11- 86 for SEQ ID NO:6, 38-113 for SEQ ID NO:7, and 58-133 for SEQ ID NO:8.
  • GI#s 14719414 and 4758122 (SEQ ID Nos:9 and 10, respectively), each have an RNA recognition motif (PFAM00076) located approximately at amino acids 35-105 for SEQ ID NO:9 and 42-110 for SEQ ID NO: 10.
  • 33 P-labeled MP21 peptide is added in an assay buffer (100 mM KC1, 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 p21 modulating agents.
  • NCI National Cancer Institute
  • ATCC American Type Culture Collection, Manassas, VA 20110-2209
  • Normal and tumor tissues were obtained from Impath, UC Davis, Clontech, Stratagene, Ardais, Genome Collaborative, and Ambion.
  • TaqMan analysis was used to assess expression levels of the disclosed genes in various samples.
  • Primers for expression analysis using TaqMan assay were prepared according to the TaqMan protocols, and the following criteria: a) primer pairs were designed to span introns to eliminate genomic contamination, and b) each primer pair produced only one product. Expression analysis was performed using a 7900HT instrument.
  • 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). For each expression analysis, 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. In cases where normal tissue was not available, a universal pool of cDNA samples was used instead. In these cases, 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 1.
  • a modulator identified by an assay desc ⁇ bed 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.
  • 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 0 diagnostic marker for disease progression
  • the assay can be performed by expression analysis as desc ⁇ bed above, by antibody directed to the gene target, or by any other available detection method.

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Abstract

Les gènes MP21 humains sont identifiés comme modulateurs de la voie p21 et ils constituent par conséquent des agents thérapeutiques pour les troubles associés à une fonction p21 défectueuse. Cette invention concerne des procédés servant à identifier des modulateurs de la protéine p21, ces procédés consistant à effectuer le criblage d'agents qui modulent l'activité du gène MP21.
PCT/US2003/006088 2002-03-01 2003-02-28 Genes mp21 utilises comme modificateurs de la voie p21 et procedes d'utilisation correspondants WO2003074663A2 (fr)

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US5958697A (en) * 1997-12-08 1999-09-28 Tularik Inc. Isolated nucleic acids encoding CYP7 promoter-binding factors

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US5958697A (en) * 1997-12-08 1999-09-28 Tularik Inc. Isolated nucleic acids encoding CYP7 promoter-binding factors

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