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  • G01N33/502—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 non-proliferative effects
  • G01N33/5041—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 non-proliferative effects involving analysis of members of signalling pathways
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  • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
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  • G01N33/57407—Specifically defined cancers
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  • G01N33/57407—Specifically defined cancers
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  • G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
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  • 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/Waf1/Cip1, cyclin G, Bax, IGF-BP3, and MDM2 (Levine, Cell (1997) 88:323-331).
• Sphingosine-1-phosphate is a lipid messenger containing both intracellular and extracellular functions. Intracellularly, it mediates proliferation and survival, and extracellularly, it is a ligand for EDG1 (Meyer zu Heringdorf, D. et al. (2001) Eur J Pharmacol 414, 145-54; Ancellin, N. et al. (2002) J Biol Chem 277, 6667-75).
• a variety of stimuli can increase cellular levels of SPP by activating sphingosine kinase (SPHK), the enzyme that initiates the phosphorylation of sphingosine.
• SPHK sphingosine kinase
• Inhibitors of SPHK can block formation of SPP and inhibit cellular proliferation induced by a variety of factors, including platelet-derived growth factor and serum (Banno, Y. et al. (1998) Biochem J 335, 3014).
• Sphingosine kinase-1 (SPHK1) phosphorylates sphingosine to form sphingosine 1-phosphate, a lipid messenger mediating signaling pathways involved in diverse functions like regulating intracellular Ca 2+ mobilization and cell proliferation and cell survival (Meyer zu Heringdorf, D. et al. (1998) Embo Journal 17, 2830-7; Nava, V. et al. (2000) FEBS Lett 473, 814).
• Sphingosine kinase 2 (SPHK2) phosphorylates sphingosine to form sphingosine 1-phosphate, which functions as a second messenger regulating proliferation and survival, as well as a ligand for selected G protein-coupled receptors (Meyer zu Heringdorf, D. et al. (1998) supra; Nava, V. et al. (2000) supra; Liu, H. et al. (2000) J Biol Chem; 275(26): 19513-20). Expression of SPHK2 in BEK 293 cells elevates SPP levels (Liu, H. et al. (2000) supra).
• SPHK sequences are highly conserved among evolutionarily diverse organisms such as human, Caenorhabditis elegans , and yeast (Kohama, T. et al. (1998) J. Biol. Chem. 273: 23722-23728).
• model organisms such as C. elegans
• C. elegans The ability to manipulate the genomes of model organisms such as C. elegans 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, Dulubova I, et al, J Neurochem 2001 April; 77(1):229-38; Cai T, et al., Diabetologia 2001 January; 44(1):81-8; Pasquinelli A E, et al., Nature.
• 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.
• SPHK genes that modify the p53 pathway in C. elegans , and identified their human orthologs, hereinafter referred to as SPHK.
• the invention provides methods for utilizing these p53 modifier genes and polypeptides to identify SPHK-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 SPHK function.
• Preferred SPHK-modulating agents specifically bind to SPHK polypeptides and restore p53 function.
• Other preferred SPHK-modulating agents are nucleic acid modulators such as antisense oligomers and RNAi that repress SPHK gene expression or product activity by, for example, binding to and inhibiting the respective nucleic acid (i.e. DNA or mRNA).
• SPHK modulating agents may be evaluated by any convenient in vitro or in vivo assay for molecular interaction with an SPHK polypeptide or nucleic acid.
• candidate SPHK modulating agents are tested with an assay system comprising a SPHK 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.
• SPHK-modulating agents include SPHK related proteins (e.g. dominant negative mutants, and biotherapeutics); SPHK-specific antibodies; SPHK-specific antisense oligomers and other nucleic acid modulators; and chemical agents that specifically bind to or interact with SPHK or compete with SPHK binding partner (e.g.
• a small molecule modulator is identified using a kinase assay.
• the screening assay system is selected from a binding assay, 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 SPHK function and/or the p53 pathway in a mammalian cell by contacting the mammalian cell with an agent that specifically binds a SPHK 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.
• RNA inhibition Methods for using RNAi to silence genes in C. elegans are known in the art (Fire A, et al., 1998 Nature 391:806-811; Fire, A. Trends Genet. 15, 358-363 (1999); WO9932619). Genes causing altered phenotypes in the worms were identified as modifiers of the p53 pathway. A modifier of particular interest, C34C6.5 was identified followed by identification of its human orthologs.
• vertebrate orthologs of these modifiers and preferably the human orthologs, sphingosine kinase (SPHK) genes (i.e., nucleic acids and polypeptides) are attractive drug targets for the treatment of pathologies associated with a defective p53 signaling pathway, such as cancer.
• SPHK sphingosine kinase
• SPHK modulating agents that act by inhibiting or enhancing SPHK expression, directly or indirectly, for example, by affecting an SPHK function such as enzymatic (e.g., catalytic) or binding activity, can be identified using methods provided herein. SPHK modulating agents are useful in diagnosis, therapy and pharmaceutical development.
• Genbank referenced by Genbank identifier (GI) number
• GI#s 11464966 SEQ ID NO:1
• 9910561 SEQ ID NO:3
• 19923819 SEQ ID NO:4
• 12052923 SEQ ID NO:6
• 13359166 SEQ ID NO:7
• 18594429 SEQ ID NO:8
• 12232440 SEQ ID NO:9
• GI#s 11464967 SEQ ID NO:10
• sequences of clones N18H08 (SEQ ID NO:2) and N31F03 SEQ D NO:5
• sequences of clones N18H08 SEQ ID NO:2
• N31F03 SEQ D NO:5
• SPHKs are kinase proteins with kinase domains.
• SPHK polypeptide refers to a full-length SPHK protein or a functionally active fragment or derivative thereof.
• a “functionally active” SPHK fragment or derivative exhibits one or more functional activities associated with a full-length, wild-type SPHK protein, such as antigenic or immunogenic activity, enzymatic activity, ability to bind natural cellular substrates, etc.
• the functional activity of SPHK 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.
• functionally active fragments also include those fragments that comprise one or more structural domains of an SPHK, such as a kinase domain or a binding domain.
• Protein domains can be identified using the PFAM program (Bateman A., et al., Nucleic Acids Res, 1999, 27:260-2).
• the kinase domains of SPHKs from GI#s 11461967, 9910562, and 20336726 are located respectively at approximately amino acid residues 16-153, 146 to 283, and 132 to 278. Methods for obtaining SPHK 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:10, 11, 12, or 13 (an SPHK).
• the fragment comprises the entire kinase (functionally active) domain.
• SPHK nucleic acid refers to a DNA or RNA molecule that encodes a SPHK polypeptide.
• the SPHK 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 SPHK.
• 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 M A and Bork P, Proc Natl Acad Sci (1998) 95:5849-5856; Huynen M A et al., Genome Research (2000) 10: 1204-1210).
• Programs for multiple sequence alignment such as CLUSTAL (Thompson J D 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 C. elegans , 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-2.0a19 (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 SEQ ID NOs:1, 2, 3, 4, 5, 6, 7, 8, or 9.
• 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 al., 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:1, 2, 3, 4, 5, 6, 7, 8, or 9 under stringent hybridization conditions that comprise: prehybridization of filters containing nucleic acid for 8 hours to overnight at 65° C. in a solution comprising 6 ⁇ single strength citrate (SSC) (1 ⁇ SSC is 0.15 M NaCl, 0.015 M Na citrate; pH 7.0), 5 ⁇ Denhardt's solution, 0.05% sodium pyrophosphate and 100 ⁇ g/ml herring sperm DNA; hybridization for 18-20 hours at 65° C.
• SSC single strength citrate
• moderately stringent hybridization conditions comprise: pretreatment of filters containing nucleic acid for 6 h at 40° C. in a solution containing 35% formamide, 5 ⁇ SSC, 50 mM Tris-HCl (pH7.5), 5 mM EDTA, 0.1% PVP, 0.1% Ficoll, 1% BSA, and 500 ⁇ g/ml denatured salmon sperm DNA; hybridization for 18-20 h at 40° C.
• low stringency conditions can be used that comprise: incubation for 8 hours to overnight at 37° C. in a solution comprising 20% formamide, 5 ⁇ SSC, 50 mM sodium phosphate (pH 7.6), 5 ⁇ 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 ⁇ SSC at about 37° C. for 1 hour.
• SPHK nucleic acids and polypeptides useful for identifying and testing agents that modulate SPHK function and for other applications related to the involvement of SPHK in the p53 pathway.
• SPHK 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 SPHK protein for assays used to assess SPHK function, such as involvement in cell cycle regulation or hypoxic response, may require expression in eukaryotic cell lines capable of these cellular activities.
• 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
• the recombinant cells are used in cell-based screening assay systems of the invention, as described further below.
• the nucleotide sequence encoding an SPHK polypeptide can be inserted into any appropriate expression vector.
• the necessary transcriptional and translational signals can derive from the native SPHK 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. 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.
• a 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 SPHK 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 SPHK gene product based on the physical or functional properties of the SPHK protein in in vitro assay systems (e.g. immunoassays).
• the SPHK 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 SPHK 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.
• 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 SPHK 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 SPHK in a p53 pathway process such as apoptosis or cell proliferation.
• the altered SPHK expression results in a detectable phenotype, such as decreased or increased levels of cell proliferation, angiogenesis, or apoptosis compared to control animals having normal SPHK 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), cows, horses, goats, sheep, pigs, dogs and cats.
• Preferred non-mammalian species include zebrafish, C. elegans , and Drosophila .
• 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.
• 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. No.
• Clones of the nonhuman transgenic animals can be produced according to available methods (see Wilmut, I. et al. (1997) 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 SPHK gene that results in a decrease of SPHK function, preferably such that SPHK 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 SPHK gene is used to construct a homologous recombination vector suitable for altering an endogenous SPHK 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 M H et al., (1994) Scan J Immunol 40:257-264; Declerck P J 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 SPHK gene, e.g., by introduction of additional copies of SPHK, or by operatively inserting a regulatory sequence that provides for altered expression of an endogenous copy of the SPHK 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 P1 (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 SPHK function and phenotypic changes are compared with appropriate control animals such as genetically modified animals that receive placebo treatment, and/or animals with unaltered SPHK expression that receive candidate therapeutic agent.
• animal models having defective p53 function can be used in the methods of the present invention.
• 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 SPHK 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 SPHK 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 SPHK activity by administering a SPHK-interacting or -modulating agent.
• an “SPHK-modulating agent” is any agent that modulated SPHK function, for example, an agent that interacts with SPHK to inhibit or enhance SPHK activity or otherwise affect normal SPHK function.
• SPHK function can be affected at any level, including transcription, protein expression, protein localization, and cellular or extra-cellular activity.
• the SPHK—modulating agent specifically modulates the function of the SPHK.
• the phrases “specific modulating agent”, “specifically modulates”, etc., are used herein to refer to modulating agents that directly bind to the SPHK polypeptide or nucleic acid, and preferably inhibit, enhance, or otherwise alter, the function of the SPHK.
• the SPHK-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 SPHK-modulating agents include small molecule compounds; SPHK-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 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 SPHK protein or may be identified by screening compound libraries.
• Alternative appropriate 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 SPHK-modulating activity. Methods for generating and obtaining compounds are well known in the art (Schreiber S L, 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.
• SPHK-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 SPHK-modulating agents.
• SPHK-interacting proteins affect normal SPHK function, including transcription, protein expression, protein localization, and cellular or extra-cellular activity.
• SPHK-interacting proteins are useful in detecting and providing information about the function of SPHK proteins, as is relevant to p53 related disorders, such as cancer (e.g., for diagnostic means).
• An SPHK-interacting protein may be endogenous, i.e. one that naturally interacts genetically or biochemically with an SPHK, such as a member of the SPHK pathway that modulates SPHK expression, localization, and/or activity.
• SPHK-modulators include dominant negative forms of SPHK-interacting proteins and of SPHK proteins themselves.
• Yeast two-hybrid and variant screens offer preferred methods for identifying endogenous SPHK-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 J R 3 rd , Trends Genet (2000) 16:5-8).
• An SPHK-interacting protein may be an exogenous protein, such as an SPHK-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, N.Y.: Cold Spring Harbor Laboratory Press). SPHK antibodies are further discussed below.
• an SPHK-interacting protein specifically binds an SPHK protein.
• an SPHK-modulating agent binds an SPHK substrate, binding partner, or cofactor.
• the protein modulator is an SPHK specific antibody agonist or antagonist.
• the antibodies have therapeutic and diagnostic utilities, and can be used in screening assays to identify SPHK modulators.
• the antibodies can also be used in dissecting the portions of the SPHK pathway responsible for various cellular responses and in the general processing and maturation of the SPHK.
• Antibodies that specifically bind SPHK polypeptides can be generated using known methods.
• the antibody is specific to a mammalian ortholog of SPHK polypeptide, and more preferably, to human SPHK.
• 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 SPHK which are particularly antigenic can be selected, for example, by routine screening of SPHK polypeptides for antigenicity or by applying a theoretical method for selecting antigenic regions of a protein (Hopp and Wood (1981), Proc. Natl. 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:10, 11, 12, or 13.
• 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 SPHK or substantially purified fragments thereof. If SPHK fragments are used, they preferably comprise at least 10, and more preferably, at least 20 contiguous amino acids of an SPHK protein.
• SPHK-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.
• SPHK-specific antibodies is assayed by an appropriate assay such as a solid phase enzyme-linked immunosorbant assay (ELISA) using immobilized corresponding SPHK polypeptides.
• an appropriate assay such as a solid phase enzyme-linked immunosorbant assay (ELISA) using immobilized corresponding SPHK polypeptides.
• ELISA enzyme-linked immunosorbant assay
• Other assays such as radioimmunoassays or fluorescent assays might also be used.
• Chimeric antibodies specific to SPHK 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 L M, 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 M S, and Queen C. 1991 Nature 351: 501-501; Morrison S L. 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).
• SPHK-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 about 10 mg/ml. Immunotherapeutic methods are further described in the literature (U.S. Pat. No. 5,859,206; WO0073469).
• SPHK-modulating agents comprise nucleic acid molecules, such as antisense oligomers or double stranded RNA (dsRNA), which generally inhibit SPHK activity.
• Preferred nucleic acid modulators interfere with the function of the SPHK nucleic acid such as DNA replication, transcription, translocation of the SPHK RNA to the site of protein translation, translation of protein from the SPHK RNA, splicing of the SPHK RNA to yield one or more mRNA species, or catalytic activity which may be engaged in or facilitated by the SPHK RNA.
• the antisense oligomer is an oligonucleotide that is sufficiently complementary to an SPHK mRNA to bind to and prevent translation, preferably by binding to the 5′ untranslated region.
• SPHK-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 J C, Antisense Oligodeoxynucleotide and Ribozyme Design, Methods.
• 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 J F, et al, Current Concepts in Antisense Drug Design, J Med Chem.
• an SPHK-specific nucleic acid modulator is used in an assay to further elucidate the role of the SPHK in the p53 pathway, and/or its relationship to other members of the pathway.
• an SPHK-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 SPHK nucleic acid or protein.
• secondary assays further assess the activity of a SPHK modulating agent identified by a primary assay and may confirm that the modulating agent affects SPHK in a manner relevant to the p53 pathway. In some cases, SPHK modulators will be directly tested in a secondary assay.
• the screening method comprises contacting a suitable assay system comprising an SPHK 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. kinase activity), which is based on the particular molecular event the screening method detects.
• a reference activity e.g. kinase activity
• a statistically significant difference between the agent-biased activity and the reference activity indicates that the candidate agent modulates SPHK activity, and hence the p53 pathway.
• the SPHK 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 G S 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 SPHK 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 SPHK-interacting proteins are used in screens to identify small molecule modulators, the binding specificity of the interacting protein to the SPHK 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 ⁇ 1
• immunogenicity e.g. ability to elicit SPHK 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 SPHK polypeptide, a fusion protein thereof, or to cells or membranes bearing the polypeptide or fusion protein.
• the SPHK polypeptide can be full length or a fragment thereof that retains functional SPHK activity.
• the SPHK polypeptide may be fused to another polypeptide, such as a peptide tag for detection or anchoring, or to another tag.
• the SPHK polypeptide is preferably human SPHK, or is an ortholog or derivative thereof as described above.
• the screening assay detects candidate agent-based modulation of SPHK interaction with a binding target, such as an endogenous or exogenous protein or other substrate that has SPHK-specific binding activity, and can be used to assess normal SPHK gene function.
• screening assays are high throughput or ultra high throughput and thus provide automated, cost-effective means of screening compound libraries for lead compounds (Fernandes P B, Curr Opin Chem Biol (1998) 2:597-603; Sundberg S A, 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 SPHK and p53 pathway modulators (e.g. U.S. Pat. No. 6,165,992 (kinase assays); U.S. Pat. Nos. 5,550,019 and 6,133,437 (apoptosis assays); U.S. Pat. No. 6,020,135 (p53 modulation), among others). Specific preferred assays are described in more detail below.
• the screening assay detects the ability of the test agent to modulate the kinase activity of an SPHK polypeptide.
• a cell-free kinase assay system is used to identify a candidate p53 modulating agent, and a secondary, cell-based assay, such as an apoptosis or hypoxic induction assay (described below), may be used to further characterize the candidate p53 modulating agent.
• apoptosis or hypoxic induction assay described below
• Radioassays which monitor the transfer of a gamma phosphate are frequently used.
• a scintillation assay for p56 (lck) kinase activity monitors the transfer of the gamma phosphate from gamma- 33 P ATP to a biotinylated peptide substrate; the substrate is captured on a streptavidin coated bead that transmits the signal (Beveridge M et al., J Biomol Screen (2000) 5:205-212).
• This assay uses the scintillation proximity assay (SPA), in which only radio-ligand bound to receptors tethered to the surface of an SPA bead are detected by the scintillant immobilized within it, allowing binding to be measured without separation of bound from free ligand.
• SPA scintillation proximity assay
• kinase receptor activation measures receptor tyrosine kinase activity by ligand stimulating the intact receptor in cultured cells, then capturing solubilized receptor with specific antibodies and quantifying phosphorylation via phosphotyrosine ELISA (Sadick M D, Dev Biol Stand (1999) 97:121-133).
• TRF time-resolved fluorometry
• This method utilizes europium chelate-labeled anti-phosphotyrosine antibodies to detect phosphate transfer to a polymeric substrate coated onto microtiter plate wells. The amount of phosphorylation is then detected using time-resolved, dissociation-enhanced fluorescence (Braunwalder A F, et al., Anal Biochem 1996 Jul. 1; 238(2):159-64).
• 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 SPHK, 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 SPHK function plays a direct role in apoptosis.
• an apoptosis assay may be performed on cells that over- or under-express SPHK relative to wild type cells. Differences in apoptotic response compared to wild type cells suggests that the SPHK plays a direct role in the apoptotic response. Apoptosis assays are described further in U.S. 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 L S 3800 Liquid Scintillation Counter).
• 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 SPHK 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 J W et al. (1986) Int J Radiat Biol Relat Stud Phys Chem Med 49:237-55). Cells transfected with an SPHK may be stained with propidium iodide and evaluated in a flow cytometer (available from Becton Dickinson).
• a cell proliferation or cell cycle assay system may comprise a cell that expresses an SPHK, 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 kinase assay system.
• a cell proliferation assay may also be used to test whether SPHK 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 SPHK relative to wild type cells. Differences in proliferation or cell cycle compared to wild type cells suggests that the SPHK 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 SPHK, 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 SPHK function plays a direct role in cell proliferation. For example, an angiogenesis assay may be performed on cells that over- or under-express SPHK relative to wild type cells. Differences in angiogenesis compared to wild type cells suggests that the SPHK 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 VEGF.
• Induction of such genes by hypoxic conditions may be assayed by growing cells transfected with SPHK 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 SPHK, 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 SPHK function plays a direct role in the hypoxic response.
• a hypoxic induction assay may be performed on cells that over- or under-express SPHK relative to wild type cells. Differences in hypoxic response compared to wild type cells suggests that the SPHK 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 2.5 g/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 2 ⁇ 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 J R et al., Bioconjug Chem. 2001 May-June; 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 J H 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, Mass.), 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, Calif.), 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 SPHK'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).
• 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 24 h. 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 SPHK gene expression, preferably mRNA expression.
• expression analysis comprises comparing SPHK expression in like populations of cells (e.g., two pools of cells that endogenously or recombinantly express SPHK) in the presence and absence of the nucleic acid modulator. Methods for analyzing mRNA and protein expression are well known in the art.
• Northern blotting For instance, Northern blotting, slot blotting, ribonuclease protection, quantitative RT-PCR (e.g., using the TaqMan®, PE Applied Biosystems), or microarray analysis may be used to confirm that SPHK mRNA expression is reduced in cells treated with the nucleic acid modulator (e.g., Current Protocols in Molecular Biology (1994) Ausubel F M et al., eds., John Wiley & Sons, Inc., chapter 4; Freeman W M et al., Biotechniques (1999) 26:112-125; Kallioniemi O P, Ann Med 2001, 33:142-147; Blohm D H and Guiseppi-Elie, A Curr Opin Biotechnol 2001, 12:41-47).
• the nucleic acid modulator e.g., Current Protocols in Molecular Biology (1994) Ausubel F M et al., eds., John Wiley & Sons,
• Protein expression may also be monitored. Proteins are most commonly detected with specific antibodies or antisera directed against either the SPHK 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).
• Secondary assays may be used to further assess the activity of SPHK-modulating agent identified by any of the above methods to confirm that the modulating agent affects SPHK in a manner relevant to the p53 pathway.
• SPHK-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 SPHK.
• Secondary assays generally compare like populations of cells or animals (e.g., two pools of cells or animals that endogenously or recombinantly express SPHK) in the presence and absence of the candidate modulator. In general, such assays test whether treatment of cells or animals with a candidate SPHK-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 and HT3 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 SPHK 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 SPHK.
• mice subcutaneously (SC) into female athymic nude mice (Taconic, Germantown, N.Y.) to support an intense vascular response.
• Mice with Matrigel® pellets may be dosed via oral (PO), intraperitoneal (IP), 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 SPHK is assessed via tumorigenicity assays.
• xenograft human tumors are 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 SPHK endogenously are injected in the flank, 1 ⁇ 10 5 to 1 ⁇ 10 7 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 IV, SC, IP, or PO by bolus administration.
• 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.
• immunohistochemistry staining 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.
• 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 SPHK 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 SPHK-modulating agent that modulates the p53 pathway.
• the invention further provides methods for modulating SPHK function in a cell, preferably a cell pre-determined to have defective or impaired SPHK function, by administering an SPHK-modulating agent. Additionally, the invention provides a method for treating disorders or disease associated with impaired SPHK function by administering a therapeutically effective amount of an SPHK-modulating agent.
• Various expression analysis methods can be used to diagnose whether SPHK expression occurs in a particular sample, including Northern blotting, slot blotting, ribonuclease protection, quantitative RT-PCR, and microarray analysis.
• Tissues having a disease or disorder implicating defective p53 signaling that express an SPHK are identified as amenable to treatment with an SPHK modulating agent.
• the p53 defective tissue overexpresses an SPHK 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 SPHK cDNA sequences as probes can determine whether particular tumors express or overexpress SPHK.
• the TaqMan® is used for quantitative RT-PCR analysis of SPHK expression in cell lines, normal tissues and tumor samples (PE Applied Biosystems).
• reagents such as the SPHK oligonucleotides, and antibodies directed against an SPHK, as described above for: (1) the detection of the presence of SPHK gene mutations, or the detection of either over- or under-expression of SPHK mRNA relative to the non-disorder state; (2) the detection of either an over- or an under-abundance of SPHK gene product relative to the non-disorder state; and (3) the detection of perturbations or abnormalities in the signal transduction pathway mediated by SPHK.
• the invention is drawn to a method for diagnosing a disease or disorder in a patient that is associated with alterations in SPHK expression, the method comprising: a) obtaining a biological sample from the patient; b) contacting the sample with a probe for SPHK 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.
• RNAi of various genes was carried out in worms homozygous for p53 deletion.
• p53 ( ⁇ / ⁇ ) worms have a normal phenotype, but are defective in germline apoptotic response to ionizing radiation as p53 is involved in the DNA damage response.
• worms were subject to gamma-irradiation, and phenotypes were scored.
• SPHK Human orthologs of the modifiers are referred to herein as SPHK.
• BLAST analysis (Altschul et al., supra) was employed to identify Targets from C. elegans modifiers. For example, representative sequences from SPHK, GI#s 11464967, 9910562, and 20336726 (SEQ ID NOs:10, 11, and 13, respectively), share 28%, 32%, and 28% amino acid identity, respectively, with the C. elegans C34C6.5.
• the kinase domains of SPHKs from GL#s 11461967, 9910562, and 20336726 are located respectively at approximately amino acid residues 16-153, 146 to 283, and 132 to 278
• Fluorescently-labeled SPHK 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 SPHK activity.
• 33 P-labeled SPHK 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.
• 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).
• a purified or partially purified SPHK is diluted in a suitable reaction buffer, e.g., 50 mM Hepes, pH 7.5, containing magnesium chloride or manganese chloride (1-20 mM) and a peptide or polypeptide substrate, such as myelin basic protein or casein (1-10 ⁇ g/ml).
• the final concentration of the kinase is 1-20 nM.
• the enzyme reaction is conducted in microtiter plates to facilitate optimization of reaction conditions by increasing assay throughput. A 96-well microtiter plate is employed using a final volume 30-100 ⁇ l.
• the reaction is initiated by the addition of 33 P-gamma-ATP (0.5 ⁇ Ci/ml) and incubated for 0.5 to 3 hours at room temperature.
• Negative controls are provided by the addition of EDTA, which chelates the divalent cation (Mg 2+ or Mn 2+ ) required for enzymatic activity. Following the incubation, the enzyme reaction is quenched using EDTA. Samples of the reaction are transferred to a 96-well glass fiber filter plate (MultiScreen, Millipore). The filters are subsequently washed with phosphate-buffered saline, dilute phosphoric acid (0.5%) or other suitable medium to remove excess radiolabeled ATP. Scintillation cocktail is added to the filter plate and the incorporated radioactivity is quantitated by scintillation counting (Wallac/Perkin Elmer). Activity is defined by the amount of radioactivity detected following subtraction of the negative control reaction value (EDTA quench).
• EDTA quench the amount of radioactivity detected following subtraction of the negative control reaction value
• 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.
• 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 300 nM primer and 250 nM probe, and approximately 25 ng 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 ⁇ STDEV(all normal samples)).
• Results are shown in Table 1. Data presented in bold indicate that greater than 50% of tested tumor samples of the tissue type indicated in row 1 exhibited over expression of the gene listed in column 1, relative to normal samples. Underlined data indicates that between 25% to 49% of tested tumor samples exhibited over expression.
• 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.
• 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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