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Definitions

• the present invention relates to kinase polypeptides, nucleotide sequences encoding the kinase polypeptides, as well as various products and methods useful for the diagnosis and treatment of various kinase-related diseases and conditions.
• Cellular signal transduction is a fundamental mechanism whereby external stimuli that regulate diverse cellular processes are relayed to the interior of cells.
• One of the key biochemical mechanisms of signal transduction involves the reversible phosphorylation of proteins, which enables regulation of the activity of mature proteins by altering their structure and function.
• Protein phosphorylation plays a pivotal role in cellular signal transduction.
• biological functions controlled by this type of postranslational mbdification are: cell division, differentiation and death (apoptosis); cell motility and cytoskeletal structure; control of DNA replication, transcription, splicing and translation; protein translocation events from the endoplasmic reticulum and Golgi apparatus to the membrane and extracellular space; protein nuclear import and export; regulation of metabolic reactions, etc.
• Abnormal protein phosphorylation is widely recognized to be causally linked to the etiology of many diseases including cancer as well as immunologic, neuronal and metabolic disorders. The following abbreviations are used for kinases throught this application:
• phosphate moiety modulates protein function in multiple ways.
• a common mechanism includes changes in the catalytic properties (Vmax and Km) of an enzyme, leading to its activation or inactivation.
• a second widely recognized mechanism involves promoting protein-protein interactions.
• An example of this is the tyrosine autophosphorylation of the ligand-activated EGF receptor tyrosine kinase. This event triggers the high-affinity binding to the phosphotyrosine residue on the receptor's C-terminal intracellular domain to the SH2 motif of the adaptor molecule Grb2.
• Grb2 in turn, binds through its SH3 motif to a second adaptor molecule, such as SHC.
• SHC second adaptor molecule
• Serine and threonine phosphorylation events also have been recently recognized to exert their biological function through protein- protein interaction events that are mediated by the high-affinity binding of phosphoserine and phosphothreonine to WW motifs present in a large variety of proteins (Lu, P.J. et al (1999) Science 283:1325-1328).
• a third important outcome of protein phosphorylation is changes in the subcellular localization of the substrate.
• nuclear import and export events in a large diversity of proteins are regulated by protein phosphorylation (Drier E.A. et al (1999) Genes Dev 13: 556-568).
• Protein kinases are one of the largest families of eukaryotic proteins with several hundred known members. These proteins share a 250-300 amino acid domain that can be subdivided into 12 distinct subdomains that comprise the common catalytic core structure. These conserved protein motifs have recently been exploited using PCR-based and bioinformatic strategies leading to a significant expansion of the known kinases. Multiple alignment of the sequences in the catalytic domain of protein kinases and subsequent parsimony analysis permits their segregation into sub-families of related kinases.
• kinases largely fall into two groups: those specific for phosphorylating serines and threonines, and those specific for phosphorylating tyrosines. Some kinases, referred to as “dual specificity" kinases, are able to phosphorylate on tyrosine as well as serine/threonine residues. Protein kinases can also be characterized by their location within the cell. Some kinases are transmembrane receptor-type proteins capable of directly altering their catalytic activity in response to the external environment such as the binding of a ligand. Others are non-receptor-type proteins lacking any transmembrane domain.
• kinases can be found in a variety of cellular compartments from the inner surface of the cell membrane to the nucleus.
• Many kinases are involved in regulatory cascades wherein their substrates may include other kinases whose activities are regulated by their phosphorylation state. Ultimately the activity of some downstream effector is modulated by phosphorylation resulting from activation of such a pathway.
• the conserved protein motifs of these kinases have recently been exploited using PCR-based cloning strategies leading to a significant expansion of the known kinases.
• tyrosine kinases PTK's
• dual-specificity kinases STK's
• STK's serine/threonine kinases
• the latter subfamily includes cyclic-nucleotide-dependent kinases, calciu calmodulin kinases, cyclin-dependent kinases (CDK's), MAP-kinases, serine-threonine kinase receptors, and several other less defined subfamilies.
• the protein kinases may be classified into several major groups including AGC, CAMK, Casein kinase 1, CMGC, STE, tyrosine kinases, and atypical kinases (Plowman, GD et al, Proceedings of the National Academy of Sciences, USA, Vol. 96, Issue 24, 13603- 13610, November 23, 1999; see also www.kinase.com).
• AGC AGC
• CAMK Casein kinase 1
• CMGC et al
• tyrosine kinases e.g., tyrosine kinases
• atypical kinases Plowman, GD et al, Proceedings of the National Academy of Sciences, USA, Vol. 96, Issue 24, 13603- 13610, November 23, 1999; see also www.kinase.com.
• families related to worm- or fungal-specific kinases and a family designated
• the AGC kinases are basic amino acid-directed enzymes that phosphorylate residues found proximal to Arg and Lys. Examples of this group are the G protein-coupled receptor kinases (GRKs), the cyclic nucleotide-dependent kinases (PKA, PKC, PKG), NDR or DBF2 kinases, ribosomal S6 kinases, AKT kinases, myotonic dystrophy kinases (DMPKs), MAPK interacting kinases (MNKs), MAST kinases, and Mo3Cl 1.
• GRKs G protein-coupled receptor kinases
• PKA cyclic nucleotide-dependent kinases
• DMPKs myotonic dystrophy kinases
• MNKs MAPK interacting kinases
• Mo3Cl Mo3Cl
• GPCRs heterotrimeric guanine protein coupled receptors
• Mutations in GPCRs cause a number of human diseases, including retinitis pigmentosa, stationary night blindness, color blindness , hyperfunctioning thyroid adenomas, familial precocious puberty , familial hypocalciuric hypercalcemia and neonatal severe hyperparathroidism (OMIM, http://www.ncbi.nlm.mh. gov/Omim/).
• OMIM retinitis pigmentosa
• stationary night blindness stationary night blindness
• color blindness hyperfunctioning thyroid adenomas
• familial precocious puberty familial precocious puberty
• familial hypocalciuric hypercalcemia familial hypocalciuric hypercalcemia
• OMIM neonatal severe hyperparathroidism
• PKA cAMP-dependent protein kinases
• AKT is a mammalian proto-oncoprotein regulated by phosphatidylinositol 3-kinase
• PI3-K which appears to function as a cell survival signal to protect cells from apoptosis.
• Insulin receptor, RAS, PI3-K, and PDK1 all act as upstream activators of AKT, whereas the lipid phosphatase PTEN functions as a negative regulator of the PI3-K/AKT pathway.
• Downstream targets for AKT-mediated cell survival include the pro-apoptotic factors BAD and Caspase9, and transcription factors in the forkhead family, such as DAF-16 in the worm.
• AKT is also an essential mediator in insulin signaling, in part due to its use of GSK-3 as another downstream target.
• the S6 kinases regulate a wide array of cellular processes involved in mitogenic response including protein synthesis, translation of specific mRNA species, and cell cycle progression from Gl to S phase.
• the gene has been localized to chromosomal region 17q23 and is amplified in breast cancer (Couch, et al, Cancer Res. 1999 Apr 1;59(7):1408-11).
• the CAMK kinases are also basic amino acid-directed kinases. They include the
• AMPK Ca2+/calmodulin-regulated and AMP-dependent protein kinases
• MLCK myosin light chain kinases
• MAPKAPKs MAP kinase activating protein kinases
• CHK2 checkpoint 2 kinases
• DAPKs death-associated protein kinases
• PHK phosphorylase kinase
• Rho-binding Trio kinases a "unique" family of CAMKs, and the EMK-related protein kinases.
• the EMK family of STKs are involved in the control of cell polarity, microtubule stability and cancer.
• C-TAK1 One member of the EMK family, has been reported to control entry into mitosis by activating Cdc25C which in turn dephosphorylates Cdc2.
• MAKV Also included in the EMK family is MAKV, which has been shown to be overexpressed in metastatic tumors (Dokl. Akad. Nauk 354 (4), 554-556 (1997)).
• CMGC kinases are "proline-directed" enzymes phosphorylating residues that exist in a proline-rich context. They include the cyclin-dependent kinases (CDKs), mitogen- activated protein kinases (MAPKs), GSK3s, RCKs, and CLKs. Most CMGC kinases have larger-than-average kinase domains owing to the presence of insertions within subdomains X and XI.
• CDK's play a pivotal role in the regulation of mitosis during cell division.
• the process of cell division occurs in four stages: S phase, the period during which chromosomes duplicate, G2, mitosis and Gl or interphase.
• S phase the period during which chromosomes duplicate, G2, mitosis and Gl or interphase.
• the duplicated chromosomes are evenly segregated allowing each daughter cell to receive a complete copy of the genome.
• a key mitotic regulator in all eukaryotic cells is the STK cdc2, a CDK regulated by cyclin B.
• some CDK-like kinases, such as CDK5 are not cyclin associated nor are they cell cycle regulated.
• MAPKs play a pivotal role in many cellular signaling pathways, including stress response and mitogenesis (Lewis, T. S., Shapiro, P. S., and Ahn, N. G. (1998) Adv. Cancer Res. 74, 49-139).
• MAP kinases can be activated by growth factors such as EGF, and cytokines such as TNF-alpha.
• EGF EGF
• cytokines TNF-alpha
• Ras becomes activated and recruits Rafl to the membrane where Rafl is activated by mechanisms that may involve phosphorylation and conformational changes (Morrison, D. K, and Cutler, R. E. (1997) Curr. Opin. CellBiol 9, 174-179).
• Active Rafl phosphorylates MEKl which in turn phosphorylates and activates the ERKs.
• the tyrosine kinase group encompass both cytoplasmic (e.g. src) as well as transmembrane receptor tyrosine kinases (e.g. EGF receptor). These kinases play a pivotal role in the signal transduction processes that mediate cell proliferation, differentiation and apoptosis.
• cytoplasmic e.g. src
• EGF receptor transmembrane receptor tyrosine kinases
• RET kinase is related to the human RET kinase. Mutations of the RET gene, encoding a receptor tyrosine kinase, have been associated with the inherited cancer syndromes MEN 2 A and MEN 2B. They have also further been associated with both familial and sporadic medullary thyroid carcinomas.
• the kinase activity can be aberrantly activated by missense mutations affecting cysteine residues within the extracellular domain, leading to potent oncogenic
• the STE family refers to the 3 classes of protein kinases that lie sequentially upstream of the MAPKs. This group includes STE7 (MEK or MAPKK) kinases, STE11 (MEKK or MAPKKK) kinases and STE20 (MEKKK) kinases.
• STE7 MEK or MAPKK
• STE11 MEKK or MAPKKK
• MEKKK MAPKKK
• STE20 MEKKK
• the prototype STE20 from baker's yeast is regulated by a hormone receptor, signaling to directly affect cell cycle progression through modulation of CDK activity. It also coordinately regulates changes in the cytoskeleton and in transcriptional programs in a bifurcating pathway.
• the homologous kinases in humans are likely to play a role in extracellular regulation of growth, cell adhesion and migration, and changes in transcriptional programs, all three of which have critical roles in tumorigenesis.
• Mammalian STE20-related protein kinases have been implicated in response to growth factors or cytokines, oxidative-, UV-, or irradiation-related stress pathways, inflammatory signals (e.g. TNF ⁇ ), apoptotic stimuli (e.g.
• the STE20-related kinases serve as upstream regulators of MAPK cascades.
• HPK1 a protein- serine/threonine kinase (STK) that possesses a STE20-like kinase domain that activates a protein kinase pathway leading to the stress-activated protein kinase SAPK JNK
• PAK1 an STK with an upstream CDC42-binding domain that interacts with Rac and plays a role in cellular transformation through the Ras-MAPK pathway
• murine NIK which interacts with upstream receptor tyrosine kinases and connects with downstream STE11 -family kinases.
• NEK kinases are related to NIMA, which is required for entry into mitosis in the filamentous fungus A. nidulans. Mutations in the nimA gene cause the nim (never in mitosis) G2 arrest phenotype in this fungus (Fry, A.M. and Nigg, E.A. (1995) Current Biology 5: 1122-1125).
• NIMA neuropeptide-like kinases
• NIMA-like kinase exists in another eukaryote besides Aspergillus, Saccharomyces pombe (Krien, M.J.E. et ⁇ /.(1998) J Cell Sci. Ill, 967-976).
• NIMA-like kinases Four mammalian NIMA-like kinases have been identified. NEK1, NEK2, NEK3 and NRK2. Despite the similarity of the NDVLA-related kinases to NIMA over the catalytic region, the mammalian kinases are structurally different to NIMA over the extracatalytic regions.
• CK1 family represents a distant branch of the protein kinase family.
• the hallmarks of protein kinase subdomains VIII and IX are difficult to identify.
• One or more forms are ubiquitously distributed in mammalian tissues and cell lines.
• CK1 kinases are found in cytoplasm, in nuclei, membrane-bound, and associated with the cytoskeleton. Splice variants differ in their subcellular distribution.
• CHKl Elongation 2 factor kinases
• SE yeast sterile family kinases
• MAPKs Caspasmodic factor kinases
• CAMKK Calcium-calmodulin kinase kinases
• DRRK dual-specific tyrosine kinases
• IKK IkB kinases
• IRAK Integrin receptor kinase
• IRE endoribonuclease-associated kinases
• MLK LIM-domain containing kinase
• MOS PIM; Receptor interacting kinase (RIP); SR-protein specific kinase (SRPK); RAF; Serine- threonine kinase receptors (STKR); TAKl; Testis specific kinas
• RIP2 is a serine-threonine kinase associated with the tumor necrosis factor (TNF) receptor complex and is implicated in the activation of NF-kappa B and cell death in mammalian cells. It has recently been demonstrated that RIP2 activates the MAPK pathway (Navas, et al, JBiol. Chem. 1999 Nov 19;274(47):33684-33690). RIP2 activates AP-1 and serum response element regulated expression by inducing the activation of the Elkl transcription factor. RIP2 directly phosphorylates and activates ERK2 in vivo and in vitro. RIP2 in turn is activated through its interaction with Ras-activated Rafl .
• TNF tumor necrosis factor
• TSL tousled
• TSL encodes a serine/threonine kinase that is essential for proper flower development.
• Human tousled-like kinases (Tlks) are cell-cycle-regulated enzymes, displaying maximal activities during S phase. This regulated activity suggests that Tlk function is linked to ongoing DNA replication (Sillje, et al, EMBO J 1999 Oct 15;18(20):5691-5702).
• proteins with protein kinase activity that appear structurally unrelated to the eukaryotic protein kinases. These include; Dictyostelium myosin heavy chain kinase A (MHCKA), Physarum polycephalum actin-fragmin kinase, the human A6 PTK, human BCR, mitochondrial pyruvate dehydrogenase and branched chain fatty acid dehydrogenase kinase, and the prokaryotic "histidine” protein kinase family.
• MHCKA Dictyostelium myosin heavy chain kinase A
• Physarum polycephalum actin-fragmin kinase Physarum polycephalum actin-fragmin kinase
• human A6 PTK Physarum polycephalum actin-fragmin kinase
• human BCR mitochondrial pyruvate dehydrogenase and branched chain
• the slime mold, worm, and human eEF-2 kinase homologues have all been demonstrated to have protein kinase activity, yet they bear little resemblance to conventional protein kinases except for the presence of a putative GxGxxG ATP-binding motif.
• histidine kinases are abundant in prokaryotes, with more than 20 representatives in E. coli, and have also been identified in yeast, molds, and plants. In response to external stimuli, these kinases act as part of two-component systems to regulate DNA replication, cell division, and differentiation through phosphorylation of an aspartate in the target protein. To date, no "histidine" kinases have been identified in metazoans, although mitochondrial pyruvate dehydrogenase (PDK) and branched chain alpha-ketoacid dehydrogenase kinase (BCKD kinase), are related in sequence.
• PDK mitochondrial pyruvate dehydrogenase
• BCKD kinase branched chain alpha-ketoacid dehydrogenase kinase
• PDK and BCKD kinase represent a unique family of atypical protein kinases involved in regulation of glycolysis, the citric acid cycle, and protein synthesis during protein malnutrition. Structurally they conserve only the C-terminal portion of "histidine” kinases including the G box regions. BCKD kinase phosphorylates the El a subunit of the BCKD complex on Ser-293, proving it to be a functional protein kinase. Although no bona fide "histidine” kinase has yet been identified in humans, they do contain PDK.
• proteins contain protein kinase-like homology including: receptor guanylyl cyclases, diacylglycerol kinases, choline/ethanolamine kinases, and YLK1 -related antibiotic resistance kinases.
• receptor guanylyl cyclases diacylglycerol kinases
• choline/ethanolamine kinases YLK1 -related antibiotic resistance kinases.
• YLK1 -related antibiotic resistance kinases Each of these families contain short motifs that were recognized by our profile searches with low scoring E-values, but apriori would not be expected to function as protein kinases. Instead, the similarity could simply reflect the modular nature of protein evolution and the primal role of ATP binding in diverse phosphotransfer enzymes.
• APHs aminoglycoside phosphotransferases
• APHs identified from bacteria that are resistant to arninoglycosides such as kanamycin, gentamycin, or amikacin.
• the crystal structure of one well characterized APH reveals that it shares greater than 40% structural identity with the 2 lobed structure of the catalytic domain of cAMP-dependent protein kinase (PKA), including an N-terminal lobe composed of a 5-stranded antiparallel beta sheet and the core of the C- te ⁇ ninal lobe including several invariant segments found in all protein kinases.
• PKA cAMP-dependent protein kinase
• APHs lack the GxGxxG normally present in the loop between beta strands 1 and 2 but contain 7 of the 12 strictly conserved residues present in most protein kinases, including the HGDxxxN signature sequence in kinase subdomain VIB. Furthermore, APH also has been shown to exhibit protein-serine/threonine kinase activity, suggesting that other YLK-related molecules may indeed be functional protein kinases.
• the eukaryotic lipid kinases (PI3Ks, PI4Ks, and PIPKs) also contain several short motifs similar to protein kinases, but otherwise share minimal primary sequence similarity.
• PI3Ks, PI4Ks, and PIPKs also contain several short motifs similar to protein kinases, but otherwise share minimal primary sequence similarity.
• structural analysis of PIPKII-beta defines a conserved ATP-binding core that is strikingly similar to conventional protein kinases. Three residues are conserved among all of these enzymes including (relative to the PKA sequence) Lys-72 which binds the gamma-phosphate of ATP, Asp- 166 which is part of the HRDLK motif and Asp- 184 from the conserved Mg 4" or Mn binding DFG motif.
• the worm genome contains 12 phosphatidylinositol kinases, including 3 PI3-kinases, 2 PI4-kinases, 3 PIP5-kinases, and 4 PI3 -kinase-related kinases.
• the latter group has 4 mammalian members (DNA-PK,
• PI3 -kinases are tightly linked to protein kinase signaling, as evidenced by their involvement downstream of many growth factor receptors and as upstream activators of the cell survival response mediated by the AKT protein kinase.
• the present invention relates, in part, to human protein kinases and protein kinase-like enzymes identified from genomic sequencing.
• Tyrosine and serine/threonine kinases (PTK's and STK's) have been identified and their protein sequence predicted as part of the instant invention. Mammalian members of these families were identified through the use of a bioinformatics strategy. The partial or complete sequences of these kinases are presented here, together with their classification, predicted or deduced protein structure.
• One aspect of the invention features an identified, isolated, enriched, or purified nucleic acid molecule encoding a kinase polypeptide having an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and SEQ ID NO:4.
• nucleic acid in reference to a nucleic acid is meant that a sequence was selected from a genomic, EST, or cDNA sequence database based on it being predicted to encode a portion of a previously unknown or novel protein kinase.
• nucleic acid in reference to nucleic acid, is meant a polymer of 10 (preferably 21, more preferably 39, most preferably 75) or more nucleotides conjugated to each other, including DNA and RNA that is isolated from a natural source or that is synthesized as the sense or complementary antisense strand.
• longer nucleic acids are preferred, for example those of 300, 600, 900, 1200, 1500, or more nucleotides and/or those having at least 50%, 60%, 75%, 80%, 85%, 90%, 95% or 99% identity to a sequence selected from the group consisting of those set forth in SEQ ID NO:l and SEQ ID NO:2.
• the isolated nucleic acid of the present invention is unique in the sense that it is not found in a pure or separated state in nature.
• Use of the term "isolated” indicates that a naturally occurring sequence has been removed from its normal cellular (i.e., chromosomal) environment. Thus, the sequence may be in a cell-free solution or placed in a different cellular environment. The term does not imply that the sequence is the only nucleotide chain present, but that it is essentially free (about 90 - 95% pure at least) of non-nucleotide material naturally associated with it, and thus is distinguished from isolated chromosomes.
• enriched in reference to nucleic acid is meant that the specific DNA or RNA sequence constitutes a significantly higher fraction (2- to 5-fold) of the total DNA or RNA present in the cells or solution of interest than in normal or diseased cells or in the cells from which the sequence was taken. This could be caused by a person by preferential reduction in the amount of other DNA or RNA present, or by a preferential increase in the amount of the specific DNA or RNA sequence, or by a combination of the two. However, it should be noted that enriched does not imply that there are no other DNA or RNA sequences present, just that the relative amount of the sequence of interest has been significantly increased.
• the term "significant" is used to indicate that the level of increase is useful to the person making such an increase, and generally means an increase relative to other nucleic acids of about at least 2-fold, more preferably at least 5- to 10-fold or even more.
• the term also does not imply that there is no DNA or RNA from other sources.
• the DNA from other sources may, for example, comprise DNA from a yeast or bacterial genome, or a cloning vector such as pUC19. This term distinguishes from naturally occurring events, such as viral infection, or tumor-type growths, in which the level of one mRNA may be naturally increased relative to other species of mRNA. That is, the term is meant to cover only those situations in which a person has intervened to elevate the proportion of the desired nucleic acid.
• nucleotide sequence be in purified form.
• purified in reference to nucleic acid does not require absolute purity (such as a homogeneous preparation). Instead, it represents an indication that the sequence is relatively more pure than in the natural environment (compared to the natural level this level should be at least 2- to 5-fold greater, e.g., in terms of mg/mL).
• Individual clones isolated from a cDNA library may be purified to electrophoretic homogeneity. The claimed DNA molecules obtained from these clones could be obtained directly from total DNA or from total RNA.
• the cDNA clones are not naturally occurring, but rather are preferably obtained via manipulation of a partially purified naturally occurring substance (messenger RNA).
• messenger RNA messenger RNA
• cDNA and pure individual cDNA clones can be isolated from the synthetic library by clonal selection of the cells carrying the cDNA library.
• the process which includes the construction of a cDNA library from mRNA and isolation of distinct cDNA clones yields an approximately 10 6 -fold purification of the native message.
• purification of at least one order of magnitude, preferably two or three orders, and more preferably four or five orders of magnitude is expressly contemplated.
• a "kinase polypeptide” is meant 32 (preferably 40, more preferably 45, most preferably 55) or more contiguous amino acids in a polypeptide having an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO: 3 and SEQ ID NO:4.
• polypeptides of 100, 200, 300, 400, 450, 500, 550, 600, 700, 800, 900 or more amino acids are preferred.
• the kinase polypeptide can be encoded by a full- length nucleic acid sequence or any portion (e.g., a "fragment" as defined herein) of the full- length nucleic acid sequence, so long as a functional activity of the polypeptide is retained, including, for example, a catalytic domain, as defined herein, or a portion thereof.
• a catalytic domain as defined herein, or a portion thereof.
• One of skill in the art would be able to select those catalytic domains, or portions thereof, which exhibit a kinase or kinase-like activity, e.g., catalytic activity, as defined herein.
• substitutions may include the replacement of an amino acid by a residue having similar physicochemical properties, such as substituting one aliphatic residue (He, Val, Leu or Ala) for another, or substitution between basic residues Lys and Arg, acidic residues Glu and Asp, amide residues Gin and Asn, hydroxyl residues Ser and Tyr, or aromatic residues Phe and Tyr.
• amino acid sequence of a kinase peptide of the invention will be substantially similar to a sequence having an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and SEQ ID NO:4, or the corresponding full-length amino acid sequence, or fragments thereof.
• identity is meant a property of sequences that measures their similarity or relationship. Identity is measured by dividing the number of identical residues by the total number of residues and gaps and multiplying the product by 100. "Gaps" are spaces in an alignment that are the result of additions or deletions of amino acids. Thus, two copies of exactly the same sequence have 100% identity, but sequences that are less highly conserved, and have deletions, additions, or replacements, may have a lower degree of identity.
• Similarity is measured by dividing the number of identical residues plus the number of conservatively substituted residues (see Bowie, et al Science, 1999), 247, 1306-1310, which is incorporated herein by reference in its entirety, including any drawings, figures, or tables) by the total number of residues and gaps and multiplying the product by 100.
• the invention features isolated, enriched, or purified nucleic acid molecules encoding a kinase polypeptide comprising a nucleotide sequence that: (a) encodes a polypeptide having an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and SEQ ID NO:4; (b) is the complement of the nucleotide sequence of (a); (c) hybridizes under highly stringent conditions to the nucleotide molecule of (a) and encodes a naturally occurring kinase polypeptide; (d) encodes a polypeptide having an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO: 3 and SEQ ID NO:4, except that it lacks one or more, but not all, of the domains selected from the group consisting of an N-terminal domain, a catalytic domain, a C-terminal catalytic domain, a C-terminal domain, a coiled-coil structure region, a proline
• nucleotide sequence is the complement of another nucleotide sequence if all of the nucleotides of the first sequence are complementary to all of the nucleotides of the second sequence.
• Various low or high stringency hybridization conditions may be used depending upon the specificity and selectivity desired. These conditions are well known to those skilled in the art. Under stringent hybridization conditions only highly complementary nucleic acid sequences hybridize.
• such conditions prevent hybridization of nucleic acids having more than 1 or 2 mismatches out of 20 contiguous nucleotides, more preferably, such conditions prevent hybridization of nucleic acids having more than 1 or 2 mismatches out of 50 contiguous nucleotides, most preferably, such conditions prevent hybridization of nucleic acids having more than 1 or 2 mismatches out of 100 contiguous nucleotides. In some instances, the conditions may prevent hybridization of nucleic acids having more than 5 mismatches in the full-length sequence.
• stringent hybridization assay conditions hybridization assay conditions at least as stringent as the following: hybridization in 50% formamide, 5X SSC, 50 mM NaH2PO4, pH 6.8, 0.5%> SDS, 0.1 mg/mL sonicated salmon sperm DNA, and 5X Denhardt's solution at 42 °C overnight; washing with 2X SSC, 0.1% SDS at 45 °C; and washing with 0.2X SSC, 0.1% SDS at 45 °C.
• the second wash can be done with 0.1X SSC at a temperature up to 70 °C (Berger et al.
• N-terminal domain refers to the extracatalytic region located between the initiator methionine and the catalytic domain of the protein kinase.
• the N-terminal domain can be identified following a Smith- Waterman alignment of the protein sequence against the non-redundant protein database to define the N-terminal boundary of the catalytic domain.
• the N-terminal domain may or may not play a regulatory role in kinase function.
• PAK65 An example of a protein kinase whose N-terminal domain has been shown to play a regulatory role is PAK65, which contains a CREB motif used for Cdc42 and rac binding (Burbelo, P.D. et al. (1995) J Biol. Chem. 270, 29071-29074).
• catalytic domain refers to a region of the protein kinase that is typically 25-300 amino acids long and is responsible for carrying out the phosphate transfer reaction from a high-energy phosphate donor molecule such as ATP or GTP to itself (autophosphorylation) or to other proteins (exogenous phosphorylation).
• the catalytic domain of protein kinases is made up of 12 subdomains that contain highly conserved amino acid residues, and are responsible for proper polypeptide folding and for catalysis.
• the catalytic domain can be identified following a Smith- Waterman alignment of the protein sequence against the non-redundant protein database.
• catalytic activity defines the rate at which a kinase catalytic domain phosphorylates a substrate.
• Catalytic activity can be measured, for example, by determining the amount of a substrate converted to a phosphorylated product as a function of time.
• Catalytic activity can be measured by methods of the invention by holding time constant and determining the concentration of a phosphorylated substrate after a fixed period of time.
• Phosphorylation of a substrate occurs at the active site of a protein kinase.
• the active site is normally a cavity in which the substrate binds to the protein kinase and is phosphorylated.
• substrate refers to a molecule phosphorylated by a kinase of the invention.
• Kinases phosphorylate substrates on serine/threonine or tyrosine amino acids.
• the molecule may be another protein or a polypeptide.
• C-terminal domain refers to the region located between the catalytic domain or the last (located closest to the C-terminus) functional domain and the carboxy- terminal amino acid residue of the protein kinase.
• functional domain is meant any region of the polypeptide that may play a regulatory or catalytic role as predicted from amino acid sequence homology to other proteins or by the presence of amino acid sequences that may give rise to specific structural conformations (e.g. N-terminal domain).
• the C-terminal domain can be identified by using a Smith- Waterman alignment of the protein sequence against the non-redundant protein database to define the C-terminal boundary of the catalytic domain or of any functional C-terminal extracatalytic domain.
• the C-terminal domain may or may not play a regulatory role in kinase function.
• An example of a protein kinase whose C-terminal domain may play a regulatory role is PAK3 which contains a heterotrimeric G b subunit-binding site near its C- terminus (Leeuw, T. et al. (1998) Nature, 391, 191-195).
• the C-terminal domain may also comprise the catalytic domain (above).
• C-terminal tail refers to a C-terminal domain of a protein kinase, that by homology extends or protrudes past the C-terminal amino acid of its closest homolog.
• C-terminal tails can be identified by using a Smith- Waterman sequence alignment of the protein sequence against the non-redundant protein database, or by means of a multiple sequence alignment of homologous sequences using the DNAStar program Megalign. Depending on its length, a C-terminal tail may or may not play a regulatory role in kinase function.
• coiled-coil structure region refers to a polypeptide sequence that has a high probability of adopting a coiled-coil structure as predicted by computer algorithms such as COILS (Lupas, A. (1996) Meth. Enzymology 266:513-525). Coiled-coils are formed by two or three amphipathic ⁇ -helices in parallel. Coiled-coils can bind to coiled-coil domains of other polypeptides resulting in homo- or heterodimers (Lupas, A. (1991) Science 252:1162-1164).
• proline-rich region refers to a region of a protein kinase whose proline content over a given amino acid length is higher than the average content of this amino acid found in proteins(t.e., >10%). Proline-rich regions are easily discernable by visual inspection of amino acid sequences and quantitated by standard computer sequence analysis programs such as the DNAStar program EditSeq. Proline-rich regions have been demonstrated to participate in regulatory protein -protein interactions.
• spacer region refers to a region of the protein kinase located between predicted functional domains.
• the spacer region has no detectable homology to any amino acid sequence in the database, and can be identified by using a Smith- Waterman alignment of the protein sequence against the non-redundant protein database to define the C- and N-terminal boundaries of the flanking functional domains.
• Spacer regions may or may not play a fundamental role in protein kinase function. Precedence for the regulatory role of spacer regions in kinase function is provided by the role of the src kinase spacer in inter-domain interactions (Xu, W. et al. (1997) Nature 385:595- 602).
• Insert refers to a portion of a protein kinase that is absent from a close homolog. Inserts may or may not by the product alternative splicing of exons. Inserts can be identified by using a Smith- Waterman sequence alignment of the protein sequence against the non-redundant protein database, or by means of a multiple sequence alignment of homologous sequences using the DNAStar program Megalign. Inserts may play a functional role by presenting a new interface for protein-protein interactions, or by interfering with such interactions.
• signal transduction pathway refers to the molecules that propagate an extracellular signal through the cell membrane to become an intracellular signal. This signal can then stimulate a cellular response.
• the polypeptide molecules involved in signal transduction processes are typically receptor and non-receptor protein tyrosine kinases, receptor and non-receptor protein phosphatases, polypeptides containing SRC homology 2 and 3 domains, phosphotyrosine binding proteins (SRC homology 2 (SH2) and phosphotyrosine binding (PTB and PH) domain containing proteins), proline-rich binding proteins (SH3 domain containing proteins), GTPases, phosphodiesterases, phospholipases, prolyl isomerases, proteases, Ca2+ binding proteins, cAMP binding proteins, guanyl cyclases, adenylyl cyclases, NO generating proteins, nucleotide exchange factors, and transcription factors.
• SRC homology 2 SH2
• PTB and PH phosphotyrosine binding
• proline-rich binding proteins SH3 domain containing proteins
• GTPases phosphodiesterases
• phospholipases prolyl isomerases
• the invention features isolated, enriched, or purified nucleic acid molecules encoding kinase polypeptides, further comprising a vector or promoter effective to initiate transcription in a host cell.
• the invention also features recombinant nucleic acid, preferably in a cell or an organism.
• the recombinant nucleic acid may contain a sequence selected from the group consisting of those set forth in SEQ ID NO:l and SEQ ID NO:2, or a functional derivative thereof and a vector or a promoter effective to initiate transcription in a host cell.
• the recombinant nucleic acid can alternatively contain a transcriptional initiation region functional in a cell, a sequence complementary to an RNA sequence encoding a kinase polypeptide and a transcriptional termination region functional in a cell. Specific vectors and host cell combinations are discussed herein.
• vector relates to a single or double-stranded circular nucleic acid molecule that can be transfected into cells and replicated within or independently of a cell genome.
• a circular double-stranded nucleic acid molecule can be cut and thereby linearized upon treatment with restriction enzymes.
• restriction enzymes An assortment of nucleic acid vectors, restriction enzymes, and the knowledge of the nucleotide sequences cut by restriction enzymes are readily available to those skilled in the art.
• a nucleic acid molecule encoding a kinase can be inserted into a vector by cutting the vector with restriction enzymes and ligating the two pieces together.
• transfecting defines a number of methods to insert a nucleic acid vector or other nucleic acid molecules into a cellular organism. These methods involve a variety of techniques, such as treating the cells with high concentrations of salt, an electric field, detergent, or DMSO to render the outer membrane or wall of the cells permeable to nucleic acid molecules of interest or use of various viral transduction strategies.
• promoter refers to nucleic acid sequence needed for gene sequence expression. Promoter regions vary from organism to organism, but are well known to persons skilled in the art for different organisms. For example, in prokaryotes, the promoter region contains both the promoter (which directs the initiation of RNA transcription) as well as the DNA sequences which, when transcribed into RNA, will signal synthesis initiation. Such regions will normally include those 5'-non-coding sequences involved with initiation of transcription and translation, such as the TATA box, capping sequence, CAAT sequence, and the like.
• the isolated nucleic acid comprises, consists essentially of, or consists of a nucleic acid sequence selected from the group consisting of those set forth in SEQ ID NO:l and SEQ ID NO:2, which encodes an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO: SEQ ID NO:3 and SEQ ID NO:4 , a functional derivative thereof, or at least 35, 40, 45, 50, 60, 75, 100, 200, or 300 contiguous amino acids selected from the group consisting of those set forth in SEQ ID NO:3 and SEQ ID NO:4.
• the nucleic acid may be isolated from a natural source by cDNA cloning or by subtractive hybridization.
• the natural source may be mammalian, preferably human, preferably blood, semen or tissue, and the nucleic acid may be synthesized by the triester method or by using an automated DNA synthesizer.
• mice refers preferably to such organisms as mice, rats, rabbits, guinea pigs, sheep, and goats, more preferably to cats, dogs, monkeys, and apes, and most preferably to humans.
• the nucleic acid is a conserved or unique region, for example those useful for: the design of hybridization probes to facilitate identification and cloning of additional polypeptides, the design of PCR probes to facilitate cloning of additional polypeptides, obtaining antibodies to polypeptide regions, and designing antisense oligonucleotides .
• nucleic acid regions regions present on two or more nucleic acids encoding a kinase polypeptide, to which a particular nucleic acid sequence can hybridize under lower stringency conditions.
• lower stringency conditions suitable for screening for nucleic acid encoding kinase polypeptides are provided in Wahl et al. Meth. Enzym. 152:399-407 (1987) and in Wahl et al. Meth. Enzym. 152:415-423 (1987), which are hereby inco ⁇ orated by reference herein in its entirety, including any drawings, figures, or tables.
• conserved regions differ by no more than 5 out of 20 nucleotides, even more preferably 2 out of 20 nucleotides or most preferably 1 out of 20 nucleotides.
• unique nucleic acid region is meant a sequence present in a nucleic acid coding for a kinase polypeptide that is not present in a sequence coding for any other naturally occurring polypeptide.
• Such regions preferably encode 32 (preferably 40, more preferably 45, most preferably 55) or more contiguous amino acids, for example, an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and SEQ ID NO:4.
• a unique nucleic acid region is preferably of mammalian origin.
• nucleic acid probe for the detection of nucleic acid encoding a kinase polypeptide having an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and SEQ ID NO:4 in a sample.
• the nucleic acid probe contains a nucleotide base sequence that will hybridize to the sequence selected from the group consisting of those set forth in SEQ ID NO:l and SEQ ID NO:2, or a functional derivative thereof.
• the nucleic acid probe hybridizes to nucleic acid encoding at least 12, 32, 75, 90, 105, 120, 150, 200, 250, 300 or 350 contiguous amino acids, wherein the nucleic acid sequence is selected from the group consisting of SEQ ID NO:l and SEQ ID NO:2, or a functional derivative thereof.
• Methods for using the probes include detecting the presence or amount of kinase RNA in a sample by contacting the sample with a nucleic acid probe under conditions such that hybridization occurs and detecting the presence or amount of the probe bound to kinase RNA.
• the nucleic acid duplex formed between the probe and a nucleic acid sequence coding for a kinase polypeptide may be used in the identification of the sequence of the nucleic acid detected (Nelson et al, in Nonisotopic DNA Probe Techniques, Academic Press, San Diego, Kricka, ed., p. 275, 1992, hereby inco ⁇ orated by reference herein in its entirety, including any drawings, figures, or tables).
• Kits for performing such methods may be constructed to include a container means having disposed therein a nucleic acid probe.
• Methods for using the probes also include using these probes to find, for example, the full-length clone of each of the predicted kinases by techniques known to one skilled in the art. These clones will be useful for screening for small molecule compounds that inhibit the catalytic activity of the encoded kinase with potential utility in treating cancers, immune- related diseases and disorders, cardiovascular disease, brain or neuronal-associated diseases, and metabolic disorders.
• disorders including cancers of tissues or blood, or hematopoietic origin, particularly those involving breast, colon, lung, prostate, cervical, brain, ovarian, bladder, or kidney; central or peripheral nervous system diseases and conditions including migraine, pain, sexual dysfunction, mood disorders, attention disorders, cognition disorders, hypotension, and hypertension; psychotic and neurological disorders, including anxiety, schizophrenia, manic depression, delirium, dementia, severe mental retardation and dyskinesias, such as Huntington's disease or Tourette's Syndrome; neurodegenerative diseases including Alzheimer's, Parkinson's, multiple sclerosis, and amyotrophic lateral sclerosis; viral or non- viral infections caused by HIV-1, HIV-2 or other viral- or prion-agents or fungal- or bacterial- organisms; metabolic disorders including Diabetes and obesity and their related syndromes, among others; cardiovascular disorders including reperfusion restenosis, coronary thrombosis, clotting disorders, unregulated cell growth disorders, atherosclerosis; ocular disease including glaucoma, retin
• the invention describes a recombinant cell or tissue comprising a nucleic acid molecule encoding a kinase polypeptide having an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4.
• the nucleic acid may be under the control of the genomic regulatory elements, or may be under the control of exogenous regulatory elements including an exogenous promoter.
• exogenous it is meant a promoter that is not normally coupled in vivo transcriptionally to the coding sequence for the kinase polypeptides.
• the polypeptide is preferably a fragment of the protein encoded by an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4.
• fragment an amino acid sequence present in a kinase polypeptide.
• a sequence comprises at least 32, 45, 50, 60, 100, 200, or 300 contiguous amino acids of a sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4.
• the invention features an isolated, enriched, or purified kinase polypeptide having the amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4.
• isolated in reference to a polypeptide is meant a polymer of 6 (preferably 12, more preferably 18, most preferably 25, 32, 40, or 50) or more amino acids conjugated to each other, including polypeptides that are isolated from a natural source or that are synthesized. In certain aspects longer polypeptides are preferred, such as those comprising 100, 200, 300, 400, 450, 500, 550, 600, 700, 800, 900 or more contiguous amino acids, including an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4 .
• the isolated polypeptides of the present invention are unique in the sense that they are not found in a pure or separated state in nature.
• isolated indicates that a naturally occurring sequence has been removed from its normal cellular environment.
• the sequence may be in a cell-free solution or placed in a different cellular environment.
• the term does not imply that the sequence is the only amino acid chain present, but that it is essentially free (about 90 - 95% pure at least) of non-amino acid-based material naturally associated with it.
• enriched in reference to a polypeptide is meant that the specific amino acid sequence constitutes a significantly higher fraction (2- to 5-fold) of the total amino acid sequences present in the cells or solution of interest than in normal or diseased cells or in the cells from which the sequence was taken.
• the other source of amino acid sequences may, for example, comprise amino acid sequence encoded by a yeast or bacterial genome, or a cloning vector such as pUC19.
• the term is meant to cover only those situations in which man has intervened to increase the proportion of the desired amino acid sequence.
• an amino acid sequence be in purified form.
• purified in reference to a polypeptide does not require absolute purity (such as a homogeneous preparation); instead, it represents an indication that the sequence is relatively purer than in the natural environment. Compared to the natural level this level should be at least 2-to 5-fold greater (e.g., in terms of mg/mL). Purification of at least one order of magnitude, preferably two or three orders, and more preferably four or five orders of magnitude is expressly contemplated. The substance is preferably free of contamination at a functionally significant level, for example 90%, 95%, or 99% pure.
• the kinase polypeptide is a fragment of the protein encoded by an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4 .
• the kinase polypeptide contains at least 32, 45, 50, 60, 100, 200, or 300 contiguous amino acids of a sequence selected from the group consisting of those set forth in SEQ ID NO: 3 and 4 , or a functional derivative thereof.
• the kinase polypeptide comprises an amino acid sequence having (a) an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4 ; and (b) an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4 , except that it lacks one or more of the domains selected from the group consisting of a C-terminal catalytic domain, an N-terminal domain, a catalytic domain, a C-terminal domain, a coiled-coil structure region, a proline-rich region, a spacer region, and a C-terminal tail.
• the polypeptide can be isolated from a natural source by methods well-known in the art.
• the natural source may be mammalian, preferably human, preferably blood, semen or tissue, and the polypeptide may be synthesized using an automated polypeptide synthesizer.
• the invention includes a recombinant kinase polypeptide having (a) an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4 .
• recombinant kinase polypeptide is meant a polypeptide produced by recombinant DNA techniques such that it is distinct from a naturally occurring polypeptide either in its location (e.g., present in a different cell or tissue than found in nature), purity or structure. Generally, such a recombinant polypeptide will be present in a cell in an amount different from that normally observed in nature.
• the polypeptides to be expressed in host cells may also be fusion proteins which include regions from heterologous proteins.
• Such regions may be included to allow, e.g., secretion, improved stability, or facilitated purification of the polypeptide.
• a sequence encoding an appropriate signal peptide can be inco ⁇ orated into expression vectors.
• a DNA sequence for a signal peptide secretory leader
• a signal peptide that is functional in the intended host cell promotes extracellular secretion of the polypeptide.
• the signal sequence will be cleaved from the polypeptide upon secretion of the polypeptide from the cell.
• preferred fusion proteins can be produced in which the N-terminus of a kinase polypeptide is fused to a carrier peptide.
• the polypeptide comprises a fusion protein which includes a heterologous region used to facilitate purification of the polypeptide.
• a heterologous region used to facilitate purification of the polypeptide.
• Many of the available peptides used for such a function allow selective binding of the fusion protein to a binding partner.
• a preferred binding partner includes one or more of the IgG binding domains of protein A are easily purified to homogeneity by affinity chromatography on, for example, IgG-coupled Sepharose.
• many vectors have the advantage of carrying a stretch of histidine residues that can be expressed at the N-terminal or C-terminal end of the target protein, and thus the protein of interest can be recovered by metal chelation chromatography.
• a nucleotide sequence encoding a recognition site for a proteolytic enzyme such as enterokinase, factor X procollagenase or thrombine may immediately precede the sequence for a kinase polypeptide to permit cleavage of the fusion protein to obtain the mature kinase polypeptide.
• fusion-protein binding partners include, but are not limited to, the yeast I-factor, the honeybee melatin leader in sf9 insect cells, 6-His tag, thioredoxin tag, hemaglutinin tag, GST tag, and OmpA signal sequence tag.
• the binding partner which recognizes and binds to the peptide may be any ion, molecule or compound including metal ions (e.g., metal affinity columns), antibodies, or fragments thereof, and any protein or peptide which binds the peptide, such as the FLAG tag.
• the invention features an antibody (e.g., a monoclonal or polyclonal antibody) having specific binding affinity to a kinase polypeptide or a kinase polypeptide domain or fragment where the polypeptide is selected from the group having an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4 .
• an antibody e.g., a monoclonal or polyclonal antibody
• the polypeptide is selected from the group having an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4 .
• specific binding affinity is meant that the antibody binds to the target kinase polypeptide with greater affinity than it binds to other polypeptides under specified conditions.
• Antibodies or antibody fragments are polypeptides that contain regions that can bind other polypeptides.
• kinase polypeptide binds to a kinase polypeptide with greater affimty than it binds to other polypeptides under specified conditions.
• Antibodies can be used to identify an endogenous source of kinase polypeptides, to monitor cell cycle regulation, and for immuno-localization of kinase polypeptides within the cell.
• polyclonal refers to antibodies that are heterogenous populations of antibody molecules derived from the sera of animals immunized with an antigen or an antigenic functional derivative thereof.
• various host animals may be immunized by injection with the antigen.
• Various adjuvants may be used to increase the immunological response, depending on the host species.
• Monoclonal antibodies are substantially homogenous populations of antibodies to a particular antigen. They may be obtained by any technique which provides for the production of antibody molecules by continuous cell lines in culture. Monoclonal antibodies may be obtained by methods known to those skilled in the art (Kohler et al, Nature 256:495- 497, 1975, and U.S. Patent No. 4,37 6,110, both of which are hereby inco ⁇ orated by reference herein in their entirety including any figures, tables, or drawings).
• antibody fragment refers to a portion of an antibody, often the hypervariable region and portions of the surrounding heavy and light chains, that displays specific binding affinity for a particular molecule.
• a hypervariable region is a portion of an antibody that physically binds to the polypeptide target.
• Antibodies or antibody fragments having specific binding affinity to a kinase polypeptide of the invention may be used in methods for detecting the presence and/or amount of kinase polypeptide in a sample by probing the sample with the antibody under conditions suitable for kinase-antibody immunocomplex formation and detecting the presence and/or amount of the antibody conjugated to the kinase polypeptide.
• Diagnostic kits for performing such methods may be constructed to include antibodies or antibody fragments specific for the kinase as well as a conjugate of a binding partner of the antibodies or the antibodies themselves.
• An antibody or antibody fragment with specific binding affinity to a kinase polypeptide of the invention can be isolated, enriched, or purified from a prokaryotic or eukaryotic organism. Routine methods known to those skilled in the art enable production of antibodies or antibody fragments, in both prokaryotic and eukaryotic organisms. Purification, enrichment, and isolation of antibodies, which are polypeptide molecules, are described above.
• Antibodies having specific binding affinity to a kinase polypeptide of the invention may be used in methods for detecting the presence and/or amount of kinase polypeptide in a sample by contacting the sample with the antibody under conditions such that an immunocomplex forms and detecting the presence and/or amount of the antibody conjugated to the kinase polypeptide.
• Diagnostic kits for performing such methods may be constructed to include a first container containing the antibody and a second container having a conjugate of a binding partner of the antibody and a label, such as, for example, a radioisotope. The diagnostic kit may also include notification of an FDA approved use and instructions therefor.
• the invention features a hybridoma which produces an antibody having specific binding affinity to a kinase polypeptide or a kinase polypeptide domain, where the polypeptide is selected from the group having an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4 .
• hybrida is meant an immortalized cell line that is capable of secreting an antibody, for example an antibody to a kinase of the invention.
• the antibody to the kinase comprises a sequence of amino acids that is able to specifically bind a kinase polypeptide of the invention.
• kits comprising antibodies that bind to a polypeptide encoded by any of the nucleic acid molecules described above, and a negative control antibody.
• negative control antibody refers to an antibody derived from similar source as the antibody having specific binding affinity, but where it displays no binding affinity to a polypeptide of the invention.
• the invention features a kinase polypeptide binding agent able to bind to a kinase polypeptide selected from the group having (a) an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4 .
• the binding agent is preferably a purified antibody that recognizes an epitope present on a kinase polypeptide of the invention.
• Other binding agents include molecules that bind to kinase polypeptides and analogous molecules that bind to a kinase polypeptide. Such binding agents may be identified by using assays that measure kinase binding partner activity, such as those that measure PDGFR activity.
• the invention also features a method for screening for human cells containing a kinase polypeptide of the invention or an equivalent sequence.
• the method involves identifying the novel polypeptide in human cells using techniques that are routine and standard in the art, such as those described herein for identifying the kinases of the invention (e.g. , cloning, Southern or Northern blot analysis, in situ hybridization, PCR amplification, etc.).
• the invention features methods for identifying a substance that modulates kinase activity comprising the steps of: (a) contacting a kinase polypeptide selected from the group having an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4 with a test substance; (b) measuring the activity of said polypeptide; and (c) determining whether said substance modulates the activity of said polypeptide.
• a kinase polypeptide selected from the group having an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4 with a test substance e.
• the kinase polypeptides of the invention including, for example, a portion of a full-length sequence such as a catalytic domain or a portion thereof, are useful for the identification of a substance which modulates kinase activity.
• Those kinase polypeptides having a functional activity are useful for identifying a substance that modulates kinase activity.
• modulates refers to the ability of a compound to alter the function of a kinase of the invention.
• a modulator preferably activates or inhibits the activity of a kinase of the invention depending on the concentration of the compound exposed to the kinase.
• modulates also refers to altering the function of kinases of the invention by increasing or decreasing the probability that a complex forms between the kinase and a natural binding partner.
• a modulator preferably increases the probability that such a complex forms between the kinase and the natural binding partner, more preferably increases or decreases the probability that a complex forms between the kinase and the natural binding partner depending on the concentration of the compound exposed to the kinase, and most preferably decreases the probability that a complex forms between the kinase and the natural binding partner.
• the term “activates” refers to increasing the cellular activity of the kinase.
• the term inhibit refers to decreasing the cellular activity of the kinase.
• Kinase activity is preferably the interaction with a natural binding partner.
• the term “complex” refers to an assembly of at least two molecules bound to one another. Signal transduction complexes often contain at least two protein molecules bound to one another. For instance, a protein tyrosine receptor protein kinase, GRB2, SOS, RAF, and RAS assemble to form a signal transduction complex in response to a mitogenic ligand.
• natural binding partner refers to polypeptides, lipids, small molecules, or nucleic acids that bind to kinases in cells.
• a change in the interaction between a kinase and a natural binding partner can manifest itself as an increased or decreased probability that the interaction forms, or an increased or decreased concentration of kinase/natural binding partner complex.
• contacting refers to mixing a solution comprising the test compound with a liquid medium bathing the cells of the methods.
• the solution comprising the compound may also comprise another component, such as dimethyl sulfoxide (DMSO), which facilitates the uptake of the test compound or compounds into the cells of the methods.
• DMSO dimethyl sulfoxide
• the solution comprising the test compound may be added to the medium bathing the cells by utilizing a delivery apparatus, such as a pipette-based device or syringe-based device.
• the invention features methods for identifying a substance that modulates kinase activity in a cell comprising the steps of: (a) expressing a kinase polypeptide in a cell, wherein said polypeptide is selected from the group having an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO: 3 and 4 ; (b) adding a test substance to said cell; and (c) monitoring a change in cell phenotype or the interaction between said polypeptide and a natural binding partner.
• kinase polypeptides of the invention are useful for the identification of a substance which modulates kinase activity.
• Those kinase polypeptides having a functional activity are useful for identifying a substance that modulates kinase activity.
• the term "expressing" as used herein refers to the production of kinases of the invention from a nucleic acid vector containing kinase genes within a cell. The nucleic acid vector is transfected into cells using well known techniques in the art as described herein.
• Another aspect of the instant invention is directed to methods of identifying compounds that bind to kinase polypeptides of the present invention, comprising contacting the kinase polypeptides with a compound, and determining whether the compound binds the kinase polypeptides.
• Binding can be determined by binding assays which are well known to the skilled artisan, including, but not limited to, gel-shift assays, Western blots, radiolabeled competition assay, phage-based expression cloning, co-fractionation by chromatography, co- precipitation, cross linking, interaction trap/two-hybrid analysis, southwestern analysis, ELISA, and the like, which are described in, for example, Current Protocols in Molecular Biology, 1999, John Wiley & Sons, NY, which is inco ⁇ orated herein by reference in its entirety.
• the compounds to be screened include, but are not limited to, compounds of extracellular, intracellular, biological or chemical origin.
• the methods of the invention also embrace compounds that are attached to a label, such as a radiolabel (e.g-., I, S, P, P, H), a fluorescence label, a chemiluminescent label, an enzymic label and an immunogenic label.
• a radiolabel e.g-., I, S, P, P, H
• fluorescence label e.g-., I, S, P, P, H
• chemiluminescent label e.g-., chemiluminescent label
• an enzymic label e.g-., I, S, P, P, H
• immunogenic label e.g-., I, S, P, P, H
• the kinase polypeptides employed in such a test may either be free in solution, attached to a solid support, borne on a cell surface, located intracellularly or associated with a portion of a cell.
• One skilled in the art can, for example, measure the formation of complex
• Another aspect of the present invention is directed to methods of identifying compounds which modulate (i.e., increase or decrease) activity of a kinase polypeptide comprising contacting the kinase polypeptide with a compound, and determining whether the compound modifies activity of the kinase polypeptide.
• the kinase polypeptides of the invention include a portion of a full-length sequence, such as a catalytic domain, as defined herein. In some instances, the kinase polypeptides of the invention comprise less than the entire catalytic domain, yet exhibit kinase or kinase-like activity. These compounds are also referred to as "modulators of protein kinases.” The activity in the presence of the test compound is measured to the activity in the absence of the test compound. Where the activity of a sample containing the test compound is higher than the activity in a sample lacking the test compound, the compound will have increased the activity.
• the present invention is particularly useful for screening compounds by using a kinase polypeptide in any of a variety of drug screening techniques.
• the compounds to be screened include, but are not limited to, extracellular, intracellular, biological or chemical origin.
• the kinase polypeptide employed in such a test may be in any form, preferably, free in solution, attached to a solid support, borne on a cell surface or located intracellularly.
• One skilled in the art can, for example, measure the formation of complexes between a kinase polypeptide and the compound being tested. Alternatively, one skilled in the art can examine the diminution in complex formation between a kinase polypeptide and its substrate caused by the compound being tested.
• the activity of kinase polypeptides of the invention can be determined by, for example, examining the ability to bind or be activated by chemically synthesised peptide ligands. Alternatively, the activity of the kinase polypeptides can be assayed by examining their ability to bind metal ions such as calcium, hormones, chemokines, neuropeptides, neurotransmitters, nucleotides, lipids, odorants, and photons. Thus, modulators of the kinase polypeptide' s activity may alter a kinase function, such as a binding property of a kinase or an activity such as signal transduction or membrane localization.
• a kinase function such as a binding property of a kinase or an activity such as signal transduction or membrane localization.
• the assay may take the form of a yeast growth assay, an Aequorin assay, a Luciferase assay, a mitogenesis assay, a MAP Kinase activity assay, as well as other binding or function-based assays of kinase activity that are generally known in the art.
• the invention includes any of the receptor and non-receptor protein tyrosine kinases, receptor and non-receptor protein phosphatases, polypeptides containing SRC homology 2 and 3 domains, phosphotyrosine binding proteins (SRC homology 2 (SH2) and phosphotyrosine binding (PTB and PH) domain containing proteins), proline-rich binding proteins (SH3 domain containing proteins), GTPases, phosphodiesterases, phospholipases, prolyl isomerases, proteases, Ca2+ binding proteins, cAMP binding proteins, guanyl cyclases, adenylyl cyclases, NO generating proteins, nucleotide exchange factors, and transcription factors.
• SRC homology 2 SH2
• PTB and PH phosphotyrosine binding
• proline-rich binding proteins SH3 domain containing proteins
• GTPases phosphodiesterases
• phospholipases prolyl isomerases
• proteases Ca2+
• Biological activities of kinases according to the invention include, but are not limited to, the binding of a natural or a synthetic ligand, as well as any one of the functional activities of kinases known in the art.
• Non-limiting examples of kinase activities include transmembrane signaling of various forms, which may involve kinase binding interactions and/or the exertion of an influence over signal transduction.
• the modulators of the invention exhibit a variety of chemical structures, which can be generally grouped into mimetics of natural kinase ligands, and peptide and non-peptide allosteric effectors of kinases.
• the invention does not restrict the sources for suitable modulators, which may be obtained from natural sources such as plant, animal or mineral extracts, or non-natural sources such as small molecule libraries, including the products of combinatorial chemical approaches to library construction, and peptide libraries.
• Recombinant receptors are preferred for binding assay HTS because they allow for better specificity (higher relative purity), provide the ability to generate large amounts of receptor material, and can be used in a broad variety of formats (see Hodgson, Bio/Technology, 1992, 10, 973-980; each of which is inco ⁇ orated herein by reference in its entirety).
• heterologous systems are available for functional expression of recombinant receptors that are well known to those skilled in the art.
• Such systems include bacteria (Strosberg, et al, Trends in Pharmacological Sciences, 1992, 13, 95-98), yeast (Pausch, Trends in Biotechnology, 1997, 15, 487-494), several kinds of insect cells (Vanden Broeck, Int. Rev. Cytology, 1996, 164, 189-268), amphibian cells (Jayawickreme et al, Current Opinion in Biotechnology, 1997, 8, 629-634) and several mammalian cell lines (CHO, HEK293, COS, etc.; see Gerhardt, et al, Eur. J. Pharmacology, 1997, 334, 1-23).
• These examples do not preclude the use of other possible cell expression systems, including cell lines obtained from nematodes (PCT application WO 98/37177).
• An expressed kinase can be used for HTS binding assays in conjunction with its defined ligand, in this case the corresponding peptide that activates it.
• the identified peptide is labeled with a suitable radioisotope, including, but not limited to, 125 1, 3 H, 35 S or 32 P, by methods that are well known to those skilled in the art.
• the peptides may be labeled by well-known methods with a suitable fluorescent derivative (Baindur, et al, Drug Dev. Res., 1994, 33, 373-398; Rogers, Drug Discovery Today, 1997, 2, 156-160).
• Radioactive ligand specifically bound to the receptor in membrane preparations made from the cell line expressing the recombinant protein can be detected in HTS assays in one of several standard ways, including filtration of the receptor-ligand complex to separate bound ligand from unbound ligand (Williams, Med. Res. Rev., 1991, 11, 147-184.; Sweetnam, et al, J. Natural Products, 1993, 56, 441-455).
• Alternative methods include a scintillation proximity assay (SPA) or a FlashPlate format in which such separation is unnecessary (Nakayama, Cur. Opinion Drug Disc. Dev., 1998, 1, 85-91 Bosse, et al, J. Biomolecular Screening, 1998, 3, 285-292.).
• Binding of fluorescent ligands can be detected in various ways, including fluorescence energy transfer (FRET), direct spectrophotofluorometric analysis of bound ligand, or fluorescence polarization (Rogers, Drug Discovery Today, 1997, 2, 156-160; Hill, Cur. Opinion Drug Disc. Dev., 1998, 1, 92-97).
• FRET fluorescence energy transfer
• Differophotofluorometric analysis of bound ligand or fluorescence polarization
• the kinases and natural binding partners required for functional expression of heterologous kinase polypeptides can be native constituents of the host cell or can be introduced through well-known recombinant technology.
• the kinase polypeptides can be intact or chimeric.
• the kinase activation results in the stimulation or inhibition of other native proteins, events that can be linked to a measurable response.
• Examples of such biological responses include, but are not limited to, the following: the ability to survive in the absence of a limiting nutrient in specifically engineered yeast cells (Pausch, Trends in Biotechnology, 1997, 15, 487-494); changes in intracellular Ca 2+ concentration as measured by fluorescent dyes (Mu ⁇ hy, et al, Cur. Opinion Drug Disc. Dev., 1998, 1, 192-199). Fluorescence changes can also be used to monitor ligand-induced changes in membrane potential or intracellular pH; an automated system suitable for HTS has been described for these pu ⁇ oses (Schroeder, et al, J. Biomolecular Screening, 1996, 1, 75- 80). Assays are also available for the measurement of common second but these are not generally preferred for HTS.
• the invention contemplates a multitude of assays to screen and identify inhibitors of ligand binding to kinase polypeptides.
• the kinase polypeptide is immobilized and interaction with a binding partner is assessed in the presence and absence of a candidate modulator such as an inhibitor compound.
• interaction between the kinase polypeptide and its binding partner is assessed in a solution assay, both in the presence and absence of a candidate inhibitor compound.
• an inhibitor is identified as a compound that decreases binding between the kinase polypeptide and its natural binding partner.
• Another contemplated assay involves a variation of the di-hybrid assay wherein an inhibitor of protein/protein interactions is identified by detection of a positive signal in a transformed or transfected host cell, as described in PCT publication number WO 95/20652, published August 3, 1995 and is included by reference herein including any figures, tables, or drawings.
• Candidate modulators contemplated by the invention include compounds selected from libraries of either potential activators or potential inhibitors. There are a number of different libraries used for the identification of small molecule modulators, including: (1) chemical libraries, (2) natural product libraries, and (3) combinatorial libraries comprised of random peptides, oligonucleotides or organic molecules. Chemical libraries consist of random chemical structures, some of which are analogs of known compounds or analogs of compounds that have been identified as “hits” or “leads” in other drug discovery screens, while others are derived from natural products, and still others arise from non-directed synthetic organic chemistry.
• Natural product libraries are collections of microorganisms, animals, plants, or marine organisms which are used to create mixtures for screening by: (1) fermentation and extraction of broths from soil, plant or marine microorganisms or (2) extraction of plants or marine organisms. Natural product libraries include polyketides, non- ribosomal peptides, and variants (non-naturally occurring) thereof. For a review, see Science 282:63-68 (1998). Combinatorial libraries are composed of large numbers of peptides, oligonucleotides, or organic compounds as a mixture. These libraries are relatively easy to prepare by traditional automated synthesis methods, PCR, cloning, or proprietary synthetic methods. Of particular interest are non-peptide combinatorial libraries.
• Still other libraries of interest include peptide, protein, peptidomimetic, multiparallel synthetic collection, recombinatorial, and polypeptide libraries.
• combinatorial chemistry and libraries created therefrom see Myers, Curr. Opin. Biotechnol. 8:701-707 (1997). Identification of modulators through use of the various libraries described herein permits modification of the candidate "hit” (or “lead") to optimize the capacity of the "hit" to modulate activity.
• binding partners can be designed and include soluble forms of binding partners, as well as such binding partners as chimeric, or fusion, proteins.
• assays may be used to identify specific peptide ligands of a kinase polypeptide, including assays that identify ligands of the target protein through measuring direct binding of test ligands to the target protein, as well as assays that identify ligands of target proteins through affinity ultrafiltration with ion spray mass spectroscopy HPLC methods or other physical and analytical methods.
• binding interactions are evaluated indirectly using the yeast two-hybrid system described in Fields et al, Nature, 340:245-246 (1989), and Fields et al, Trends in Genetics, 10:286-292 (1994), both of which are inco ⁇ orated herein by reference.
• the two-hybrid system is a genetic assay for detecting interactions between two proteins or polypeptides. It can be used to identify proteins that bind to a known protein of interest, or to delineate domains or residues critical for an interaction. Variations on this methodology have been developed to clone genes that encode DNA binding proteins, to identify peptides that bind to a protein, and to screen for drugs.
• the two-hybrid system exploits the ability of a pair of interacting proteins to bring a transcription activation domain into close proximity with a DNA binding domain that binds to an upstream activation sequence (UAS) of a reporter gene, and is generally performed in yeast.
• UAS upstream activation sequence
• the assay requires the construction of two hybrid genes encoding (1) a DNA-binding domain that is fused to a first protein and (2) an activation domain fused to a second protein.
• the DNA-binding domain targets the first hybrid protein to the UAS of the reporter gene; however, because most proteins lack an activation domain, this DNA-binding hybrid protein does not activate transcription of the reporter gene.
• the second hybrid protein which contains the activation domain, cannot by itself activate expression of the reporter gene because it does not bind the UAS. However, when both hybrid proteins are present, the noncovalent interaction of the first and second proteins tethers the activation domain to the UAS, activating transcription of the reporter gene.
• this assay can be used to detect agents that interfere with the binding interaction.
• Expression of the reporter gene is monitored as different test agents are added to the system. The presence of an inhibitory agent results in lack of a reporter signal.
• the yeast two-hybrid assay can also be used to identify proteins that bind to the gene product, h an assay to identify proteins that bind to a kinase polypeptide, or fragment thereof, a fusion polynucleotide encoding both a kinase polypeptide (or fragment) and a UAS binding domain (i.e., a first protein) may be used.
• a large number of hybrid genes each encoding a different second protein fused to an activation domain are produced and screened in the assay.
• the second protein is encoded by one or more members of a total cDNA or genomic DNA fusion library, with each second protein coding region being fused to the activation domain.
• This system is applicable to a wide variety of proteins, and it is not even necessary to know the identity or function of the second binding protein.
• the system is highly sensitive and can detect interactions not revealed by other methods; even transient interactions may trigger transcription to produce a stable mRNA that can be repeatedly translated to yield the reporter protein.
• Other assays may be used to search for agents that bind to the target protein.
• One such screening method to identify direct binding of test ligands to a target protein is described in U.S. Patent No. 5,585,277, inco ⁇ orated herein by reference.
• This method relies on the principle that proteins generally exist as a mixture of folded and unfolded states, and continually alternate between the two states.
• a test ligand binds to the folded form of a target protein (i.e., when the test ligand is a ligand of the target protein)
• the target protein molecule bound by the ligand remains in its folded state.
• the folded target protein is present to a greater extent in the presence of a test ligand which binds the target protein, than in the absence of a ligand.
• Binding of the ligand to the target protein can be determined by any method which distinguishes between the folded and unfolded states of the target protein.
• the function of the target protein need not be known in order for this assay to be performed. Virtually any agent can be assessed by this method as a test ligand, including, but not limited to, metals, polypeptides, proteins, lipids, polysaccharides, polynucleotides and small organic molecules.
• methods of screening for compounds which modulate kinase activity comprise contacting test compounds with kinase polypeptides and assaying for the presence of a complex between the compound and the kinase polypeptide.
• the ligand is typically labelled. After suitable incubation, free ligand is separated from that present in bound form, and the amount of free or uncomplexed label is a measure of the ability of the particular compound to bind to the kinase polypeptide.
• high throughput screening for compounds having suitable binding affinity to kinase polypeptides is employed. Briefly, large numbers of different small peptide test compounds are synthesised on a solid substrate. The peptide test compounds are contacted with the kinase polypeptide and washed. Bound kinase polypeptide is then detected by methods well known in the art. Purified polypeptides of the invention can also be coated directly onto plates for use in the aforementioned drug screening techniques. In addition, non-neutralizing antibodies can be used to capture the protein and immobilize it on the solid support.
• inventions comprise using competitive screening assays in which neutralizing antibodies capable of binding a polypeptide of the invention specifically compete with a test compound for binding to the polypeptide.
• the antibodies can be used to detect the presence of any peptide that shares one or more antigenic determinants with a kinase polypeptide.
• Radiolabeled competitive binding studies are described in A.H. Lin et al. Antimicrobial Agents and Chemotherapy, 1997, vol. 41, no. 10. pp. 2127-2131, the disclosure of which is inco ⁇ orated herein by reference in its entirety.
• the invention provides methods for treating a disease by administering to a patient in need of such treatment a substance that modulates the activity of a kinase polypeptide selected from the group consisting of those set forth in SEQ ID NO:3 and 4 , as well as the full-length polypeptide thereof, or a portion of any of these sequences that retains functional activity, as described herein.
• a kinase polypeptide selected from the group consisting of those set forth in SEQ ID NO:3 and 4 , as well as the full-length polypeptide thereof, or a portion of any of these sequences that retains functional activity, as described herein.
• the disease is selected from the group consisting of cancers, immune-elated diseases and disorders, cardiovascular disease, brain or neuronal-associated diseases, and metabolic disorders.
• these diseases include cancer of tissues, blood, or hematopoietic origin, particularly those involving breast, colon, lung, prostate, cervical, brain, ovarian, bladder, or kidney; central or peripheral nervous system diseases and conditions including migraine, pain, sexual dysfunction, mood disorders, attention disorders, cognition disorders, hypotension, and hypertension; psychotic and neurological disorders, including anxiety, schizophrenia, manic depression, delirium, dementia, severe mental retardation and dyskinesias, such as Huntington's disease or Tourette's Syndrome; neurodegenerative diseases including Alzheimer's, Parkinson's, Multiple sclerosis, and Amyotrophic lateral sclerosis; viral or non- viral infections caused by HIV-1, HIV-2 or other viral- or prion-agents or fungal- or bacterial- organisms; metabolic disorders including Diabetes and obesity and their related syndromes, among others; cardiovascular disorders including reperfusion restenosis, coronary thrombosis, clotting disorders, unregulated cell growth disorders, atherosclerosis; ocular disease including glaucoma, retinopathy
• the invention provides methods for treating or preventing a disease or disorder by administering to a patient in need of such treatment a substance that modulates the activity of a kinase polypeptide having an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4 , as well as the full-length polypeptide thereof, or a portion of any of these sequences that retains functional activity, as described herein.
• the disease is selected from the group consisting of cancers, immune-related diseases and disorders, cardiovascular disease, brain or neuronal-associated diseases, and metabolic disorders.
• these diseases include cancer of tissues, blood, or hematopoietic origin, particularly those involving breast, colon, lung, prostate, cervical, brain, ovarian, bladder, or kidney; central or peripheral nervous system diseases and conditions including migraine, pain, sexual dysfunction, mood disorders, attention disorders, cognition disorders, hypotension, and hypertension; psychotic and neurological disorders, including anxiety, schizophrenia, manic depression, delirium, dementia, severe mental retardation and dyskinesias, such as Huntington's disease or Tourette's Syndrome; neurodegenerative diseases including Alzheimer's, Parkinson's, Multiple sclerosis, and Amyotrophic lateral sclerosis; viral or non- viral infections caused by HIV-1, HIV-2 or other viral- or prion-agents or fungal- or bacterial- organisms; metabolic disorders including Diabetes and obesity and their related syndromes, among others; cardiovascular disorders including reperfusion restenosis, coronary thrombosis, clotting disorders, unregulated cell growth disorders, atherosclerosis; ocular disease including glaucoma, retinopathy
• the invention also features methods of treating or preventing a disease or disorder by administering to a patient in need of such treatment a substance that modulates the activity of a kinase polypeptide having an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4 , as well as the full-length polypeptide thereof, or a portion of any of these sequences that retains functional activity, as described herein.
• the disease is selected from the group consisting of cancers, immune-related diseases and disorders, cardiovascular disease, brain or neuronal-associated diseases, and metabolic disorders.
• these diseases include cancer of tissues, blood, or hematopoietic origin, particularly those involving breast, colon, lung, prostate, cervical, brain, ovarian, bladder, or kidney; central or peripheral nervous system diseases and conditions including migraine, pain, sexual dysfunction, mood disorders, attention disorders, cognition disorders, hypotension, and hypertension; psychotic and neurological disorders, including anxiety, schizophrenia, manic depression, delirium, dementia, severe mental retardation and dyskinesias, such as Huntington's disease or Tourette's Syndrome; neurodegenerative diseases including Alzheimer's, Parkinson's, Multiple sclerosis, and Amyotrophic lateral sclerosis; viral or non- viral infections caused by HIV-1, HIV-2 or other viral- or prion-agents or fungal- or bacterial- organisms; metabolic disorders including Diabetes and obesity and their related syndromes, among others; cardiovascular disorders including reperfusion restenosis, coronary thrombosis, clotting disorders, unregulated cell growth disorders, atherosclerosis; ocular disease including glaucoma, retinopathy
• the invention also features methods of treating or preventing a disease or disorder by administering to a patient in need of such treatment a substance that modulates the activity of a kinase polypeptide having an amino acid sequence selected from the group consisting those set forth in SEQ ID NO:3 and 4 , as well as the full-length polypeptide thereof, or a portion of any of these sequences that retains functional activity, as described herein.
• the disease is selected from the group consisting of immune-related diseases and disorders, cardiovascular disease, and cancer.
• these diseases include cancer of tissues, blood, or hematopoietic origin, particularly those involving breast, colon, lung, prostate, cervical, brain, ovarian, bladder, or kidney; central or peripheral nervous system diseases and conditions including migraine, pain, sexual dysfunction, mood disorders, attention disorders, cognition disorders, hypotension, and hypertension; psychotic and neurological disorders, including anxiety, schizophrenia, manic depression, delirium, dementia, severe mental retardation and dyskinesias, such as Huntington's disease or Tourette's Syndrome; neurodegenerative diseases including Alzheimer's, Parkinson's, Multiple sclerosis, and
• Amyotrophic lateral sclerosis viral or non- viral infections caused by HIV-1, HIV-2 or other viral- or prion-agents or fungal- or bacterial- organisms; metabolic disorders including Diabetes and obesity and their related syndromes, among others; cardiovascular disorders including reperfusion restenosis, coronary thrombosis, clotting disorders, unregulated cell growth disorders, atherosclerosis; ocular disease including glaucoma, retinopathy, and macular degeneration; inflammatory disorders including rheumatoid arthritis, chronic inflammatory bowel disease, chronic inflammatory pelvic disease, multiple sclerosis, asthma, osteoarthritis, psoriasis, atherosclerosis, rhinitis, autoimmunity, and organ transplant rejection.
• the immune-related diseases and disorders are selected from the group consisting of rheumatoid arthritis, chronic inflammatory bowel disease, chronic inflammatory pelvic disease, multiple sclerosis, asthma, osteoarthritis, psoriasis, atherosclerosis, rhinitis, autoimmunity, and organ transplantation.
• Substances useful for treatment of kinase-related disorders or diseases preferably show positive results in one or more in vitro assays for an activity corresponding to treatment of the disease or disorder in question (Examples of such assays are provided in the references in section VI, below; and in Example 7, herein). Examples of substances that can be screened for favorable activity are provided and referenced in section VI, below.
• the substances that modulate the activity of the kinases preferably include, but are not limited to, antisense oligonucleotides and inhibitors of protein kinases, as determined by methods and screens referenced in section VI and Example 7, below.
• preventing refers to decreasing the probability that an organism contracts or develops an abnormal condition.
• treating refers to having a therapeutic effect and at least partially alleviating or abrogating an abnormal condition in the organism.
• a therapeutic effect refers to the inhibition or activation factors causing or contributing to the abnormal condition.
• a therapeutic effect relieves to some extent one or more of the symptoms of the abnormal condition.
• a therapeutic effect can refer to one or more of the following: (a) an increase in the proliferation, growth, and/or differentiation of cells; (b) inhibition (i.e., slowing or stopping) of cell death; (c) inhibition of degeneration; (d) relieving to some extent one or more of the symptoms associated with the abnormal condition; and (e) enhancing the function of the affected population of cells.
• Compounds demonstrating efficacy against abnormal conditions can be identified as described herein.
• abnormal condition refers to a function in the cells or tissues of an organism that deviates from their normal functions in that organism.
• An abnormal condition can relate to cell proliferation, cell differentiation, or cell survival.
• Abnormal cell proliferative conditions include cancers such as fibrotic and mesangial disorders, abnormal angiogenesis and vasculogenesis, wound healing, psoriasis, diabetes mellitus, and inflammation.
• Abnormal differentiation conditions include, but are not limited to neurodegenerative disorders, slow wound healing rates, and slow tissue grafting healing rates.
• Abnormal cell survival conditions relate to conditions in which programmed cell death (apoptosis) pathways are activated or abrogated.
• apoptosis programmed cell death
• a number of protein kinases are associated with the apoptosis pathways. Aberrations in the function of any one of the protein kinases could lead to cell immortality or premature cell death.
• administering relates to a method of inco ⁇ orating a compound into cells or tissues of an organism. The abnormal condition can be prevented or treated when the cells or tissues of the organism exist within the organism or outside of the organism.
• Cells existing outside the organism can be maintained or grown in cell culture dishes.
• many techniques exist in the art to administer compounds including (but not limited to) oral, parenteral, dermal, injection, and aerosol applications.
• multiple techniques exist in the art to administer the compounds including (but not limited to) cell microinjection techniques, transformation techniques, and carrier techniques.
• the abnormal condition can also be prevented or treated by administering a compound to a group of cells having an aberration in a signal transduction pathway to an organism.
• the effect of administering a compound on organism function can then be monitored.
• the organism is preferably a mouse, rat, rabbit, guinea pig, or goat, more preferably a monkey or ape, and most preferably a human.
• the invention features methods for detection of a kinase polypeptide in a sample as a diagnostic tool for diseases or disorders, wherein the method comprises the steps of: (a) contacting the sample with a nucleic acid probe which hybridizes under hybridization assay conditions to a nucleic acid target region of a kinase polypeptide having an amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4 , said probe comprising the nucleic acid sequence encoding the polypeptide, fragments thereof, and the complements of the sequences and fragments; and (b) detecting the presence or amount of the probe:target region hybrid as an indication of the disease.
• the disease or disorder is selected from the group consisting of rheumatoid arthritis, arteriosclerosis, autoimmune disorders, organ transplantation, myocardial infarction, cardiomyopathies, stroke, renal failure, oxidative stress-related neurodegenerative disorders, and cancer.
• the kinase "target region” is the nucleotide base sequence selected from the group consisting of those set forth in SEQ ID NO:l and SEQ ID NO:2, or the corresponding full- length sequences, a functional derivative thereof, or a fragment thereof, to which the nucleic acid probe will specifically hybridize. Specific hybridization indicates that in the presence of other nucleic acids the probe only hybridizes detectably with the kinase of the invention's target region.
• Putative target regions can be identified by methods well known in the art consisting of alignment and comparison of the most closely related sequences in the database.
• the nucleic acid probe hybridizes to a kinase target region encoding at least 6, 12, 75, 90, 105, 120, 150, 200, 250, 300 or 350 contiguous amino acids of a sequence selected from the group consisting of those set forth in SEQ ID NO:3 and 4 , or the corresponding full-length amino acid sequence, a portion of any of these sequences that retains functional activity, as described herein, or a functional derivative thereof.
• Hybridization conditions should be such that hybridization occurs only with the kinase genes in the presence of other nucleic acid molecules. Under stringent hybridization conditions only highly complementary nucleic acid sequences hybridize. Preferably, such conditions prevent hybridization of nucleic acids having more than 1 or 2 mismatches out of 20 contiguous nucleotides. Such conditions are defined supra.
• the diseases for which detection of kinase genes in a sample could be diagnostic include diseases in which kinase nucleic acid (DNA and/or RNA) is amplified in comparison to normal cells.
• amplification is meant increased numbers of kinase DNA or RNA in a cell compared with normal cells.
• kinases are typically found as single copy genes.
• the chromosomal location of the kinase genes may be amplified, resulting in multiple copies of the gene, or amplification.
• Gene amplification can lead to amplification of kinase RNA, or kinase RNA can be amplified in the absence of kinase DNA amplification.
• RNA can be the detectable presence of kinase RNA in cells, since in some normal cells there is no basal expression of kinase RNA. In other normal cells, a basal level of expression of kinase exists, therefore in these cases amplification is the detection of at least 1 -2-fold, and preferably more, kinase RNA, compared to the basal level.
• the diseases that could be diagnosed by detection of kinase nucleic acid in a sample preferably include cancers.
• the test samples suitable for nucleic acid probing methods of the present invention include, for example, cells or nucleic acid extracts of cells, or biological fluids.
• samples used in the above-described methods will vary based on the assay format, the detection method and the nature of the tissues, cells or extracts to be assayed.
• Methods for preparing nucleic acid extracts of cells are well known in the art and can be readily adapted in order to obtain a sample that is compatible with the method utilized.
• the invention also features a method for detection of a kinase polypeptide in a sample as a diagnostic tool for a disease or disorder, wherein the method comprises: (a) comparing a nucleic acid target region encoding the kinase polypeptide in a sample, where the kinase polypeptide has an amino acid sequence selected from the group consisting those set forth in SEQ ID NO:3 and SEQ ID NO:4 , or one or more fragments thereof, with a control nucleic acid target region encoding the kinase polypeptide, or one or more fragments thereof; and (b) detecting differences in sequence or amount between the target region and the control target region, as an indication of the disease or disorder.
• the disease is selected from the group consisting of cancers, immune-related diseases and disorders, cardiovascular disease, brain or neuronal-associated diseases, and metabolic disorders. More specifically these diseases include cancer of tissues, blood, or hematopoietic origin, particularly -those involving breast, colon, lung, prostate, cervical, brain, ovarian, bladder, or kidney; central or peripheral nervous system diseases and conditions including migraine, pain, sexual dysfunction, mood disorders, attention disorders, cognition disorders, hypotension, and hypertension; psychotic and neurological disorders, including anxiety, schizophrenia, manic depression, delirium, dementia, severe mental retardation and dyskinesias, such as Huntington's disease or Tourette's Syndrome; neurodegenerative diseases including Alzheimer's, Parkinson's, Multiple sclerosis, and Amyotrophic lateral sclerosis; viral or non-viral infections caused by HIV-1, HIV-2 or other viral- or prion-agents or fungal- or bacterial- organisms; metabolic disorders including Diabetes and obesity and their related syndromes, among others; cardiovascular disorders including reperfusion
• comparing refers to identifying discrepancies between the nucleic acid target region isolated from a sample, and the control nucleic acid target region.
• the discrepancies can be in the nucleotide sequences, e.g. insertions, deletions, or point mutations, or in the amount of a given nucleotide sequence. Methods to determine these discrepancies in sequences are well-known to one of ordinary skill in the art.
• the "control" nucleic acid target region refers to the sequence or amount of the sequence found in normal cells, e.g. cells that are not diseased as discussed previously.
• Figures 1 A and B show the nucleotide sequences for human protein kinases oriented in a 5' to 3' direction (SEQ ID NO:l, SEQ ID NO:2).
• Figures 2A and B show the amino acid sequences for the human protein kinases encoded by SEQ ID No. 1 and 2 in the direction of translation (SEQ ID NO: 3 and 4). If a predicted stop codons is within the coding region, it is indicated by an 'x.'
• the invention provides, inter alia, protein kinase and kinase-like genes, as well as fragments thereof, which have been identified in genomic databases.
• the invention provides nucleic acid molecules that are capable of encoding polypeptides having a kinase or kinase-like activity.
• genes of the invention can be better understood.
• the invention additionally provides a number of different embodiments, such as those described below.
• Nucleic Acids Associations of chromosomal localizations for mapped genes with amplicons implicated in cancer are based on literature searches (PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi), OMIM searches (Online Mendelian Inheritance in Man, http://www.ncbi.nlm.nih.gov/Omim/searchomim.html) and the comprehensive database of cancer amplicons maintained by Knuutila, et al. (Knuutila, et al., DNA copy number amplifications in human neoplasms. Review of comparative genomic hybridization studies. Am J Pathol 152:1107-1123, 1998.
• the invention additionally provides nucleic acid probes and uses therefor.
• a nucleic acid probe of the present invention may be used to probe an appropriate chromosomal or cDNA library by usual hybridization methods to obtain other nucleic acid molecules of the present invention.
• a cliromosomal DNA or cDNA library may be prepared from appropriate cells according to recognized methods in the art (cf. "Molecular Cloning: A Laboratory Manual", second edition, Cold Spring Harbor Laboratory, Sambrook, Fritsch, & Maniatis, eds., 1989).
• nucleic acid probes having nucleotide sequences which correspond to N-terminal and C-terminal portions of the amino acid sequence of the polypeptide of interest.
• the synthesized nucleic acid probes may be used as primers in a polymerase chain reaction (PCR) carried out in accordance with recognized PCR techniques, essentially according to PC Protocols, "A Guide to Methods and Applications", Academic Press, Michael, et al, eds., 1990, utilizing the appropriate chromosomal or cDNA library to obtain the fragment of the present invention.
• PCR polymerase chain reaction
• hybridization probes of the present invention can be labeled by standard labeling techniques such as with a radiolabel, enzyme label, fluorescent label, biotin-avidin label, chemiluminescence, and the like. After hybridization, the probes may be visualized using known methods.
• the nucleic acid probes of the present invention include RNA, as well as DNA probes, such probes being generated using techniques known in the art.
• the nucleic acid probe may be immobilized on a solid support.
• solid supports include, but are not limited to, plastics such as polycarbonate, complex carbohydrates such as agarose and sepharose, and acrylic resins, such as polyacrylamide and latex beads. Techniques for coupling nucleic acid probes to such solid supports are well known in the art.
• test samples suitable for nucleic acid probing methods of the present invention include, for example, cells or nucleic acid extracts of cells, or biological fluids.
• the samples used in the above-described methods will vary based on the assay format, the detection method and the nature of the tissues, cells or extracts to be assayed. Methods for preparing nucleic acid extracts of cells are well known in the art and can be readily adapted in order to obtain a sample which is compatible with the method utilized.
• One method of detecting the presence of nucleic acids of the invention in a sample comprises (a) contacting said sample with the above-described nucleic acid probe under conditions such that hybridization occurs, and (b) detecting the presence of said probe bound to said nucleic acid molecule.
• Samples to be tested include but should not be limited to RNA samples of human tissue.
• a kit for detecting the presence of nucleic acids of the invention in a sample comprises at least one container means having disposed therein the above-described nucleic acid probe.
• the kit may further comprise other containers comprising one or more of the following: wash reagents and reagents capable of detecting the presence of bound nucleic acid probe.
• detection reagents include, but are not limited to radiolabelled probes, enzymatic labeled probes (horseradish peroxidase, alkaline phosphatase), and affinity labeled probes (biotin, avidin, or steptavidin).
• the kit further comprises instructions for use.
• a compartmentalized kit includes any kit in which reagents are contained in separate containers.
• Such containers include small glass containers, plastic containers or strips of plastic or paper.
• Such containers allow the efficient transfer of reagents from one compartment to another compartment such that the samples and reagents are not cross- contaminated and the agents or solutions of each container can be added in a quantitative fashion from one compartment to another.
• Such containers will include a container which will accept the test sample, a container which contains the probe or primers used in the assay, containers which contain wash reagents (such as phosphate buffered saline, Tris-buffers, and the like), and containers which contain the reagents used to detect the hybridized probe, bound antibody, amplified product, or the like.
• nucleic acid probes described in the present invention can readily be inco ⁇ orated into one of the established kit formats which are well known in the art. CATEGORIZATION OF THE POLYPEPTIDES ACCORDING TO THE INVENTION
• a classification of the protein class and family to which it belongs a summary of non-catalytic protein motifs, as well as a chromosomal location. This information is useful in determing function, regulation and/or therapeutic utility for each of the proteins. Amplification of chromosomal region can be associated with various cancers.
• the kinase classification and protein domains often reflect pathways, cellular roles, or mechanisms of up- or down-stream regulation. Also disease-relevant genes often occur in families of related genes. For example, if one member of a kinase family functions as an oncogene, a tumor suppressor, or has been found to be disrupted in an immune, neurologic, cardiovascular, or metabolic disorder, frequently other family members may play a related role.
• the expression analysis organizes kinases into groups that are transcriptionally upregulated in tumors and those that are more restricted to specific tumor types such as melanoma or prostate.
• This analysis also identifies genes that are regulated in a cell cycle dependent manner, and are therefore likely to be involved in maintaining cell cycle checkpoints, entry, progression, or exit from mitosis, oversee DNA repair, or are involved in cell proliferation and genome stability.
• Expression data also can identify genes expressed in endothelial sources or other tissues that suggest a role in angiogenesis, thereby implicating them as targets for control of diseases that have an angiogenic component, such as cancer, endometriosis, retinopathy and macular degeneration, and various ischemic or vascular pathologies.
• a proteins' role in cell survival can also be suggested based on restricted expression in cells subjected to external stress such as oxidative damage, hypoxia, drugs such as cisplatinum, or irradiation.
• Metastases-associated genes can be implicated when expression is restricted to invading regions of a tumor, or is only seen in local or distant metastases compared to the primary tumor, or when a gene is upregulated during cell culture models of invasion, migration, or motility.
• Chromosomal location can identify candidate targets for a tumor amplicon or a tumor- suppressor locus. Summaries of prevalent tumor amplicons are available in the literature, and can identify tumor types to experimentally be confirmed to contain amplified copies of a kinase gene which localizes to an adjacent region.
• polypeptides of the present invention can be classified, for example, among two different groups.
• the salient features related to the biological and clinical implications of these different groups are described hereafter in more general terms.
• a more specific characterization of the polypeptides of the invention, including potential biological and clinical implications, is provided, e.g., in EXAMPLES 2a and 2b.
• the AGC group of protein kinases includes as its major prototypes protein kinase C (PKC), cAMP-dependent protein kinases (PKA), the G protein-coupled receptor kinases (ARK and rhodopsin kinase (GRK1)) as well as ⁇ 70S6K and AKT.
• PLC protein kinase C
• PKA cAMP-dependent protein kinases
• GRK1 G protein-coupled receptor kinases
• a novel AGC group kinase includes SEQ ID NO:4.
• the STE group of protein kinases includes, as its major prototypes, the NEK kinases, as well as the STE11 and STE20 family of sterile protein kinases.
• a novel STE protein kinase includes: SEQ ID NO: 3.
• the invention provides methods for detecting a polypeptide in a sample as a diagnostic tool for diseases or disorders, wherein the method comprises the steps of: (a) contacting the sample with a nucleic acid probe which hybridizes under hybridization assay conditions to a nucleic acid target region of a polypeptide selected from the group consisting of SEQ ID NO:3 or 4, said probe comprising the nucleic acid sequence encoding the polypeptide, fragments thereof, and the complements of the sequences and fragments; and (b) detecting the presence or amount of the probe:target region hybrid as an indication of the disease.
• the disease or disorder is selected from the group consisting of rheumatoid arthritis, atherosclerosis, autoimmune disorders, organ transplantation, myocardial infarction, cardiomyopathies, stroke, renal failure, oxidative stress-related neurodegenerative disorders, metabolic disorder including diabetes, reproductive disorders including infertility, and cancer.
• Hybridization conditions should be such that hybridization occurs only with the genes in the presence of other nucleic acid molecules. Under stringent hybridization conditions only highly complementary nucleic acid sequences hybridize. Preferably, such conditions prevent hybridization of nucleic acids having 1 or 2 mismatches out of 20 contiguous nucleotides. Such conditions are defined supra.
• RNA nucleic acid
• amplification is meant increased numbers of DNA or RNA in a cell compared with normal cells.
• Amplification as it refers to RNA can be the detectable presence of RNA in cells, since in some normal cells there is no basal expression of RNA. In other normal cells, a basal level of expression exists, therefore in these cases amplification is the detection of at least 1- 2-fold, and preferably more, compared to the basal level.
• the diseases that could be diagnosed by detection of nucleic acid in a sample preferably include cancers.
• the test samples suitable for nucleic acid probing methods of the present invention include, for example, cells or nucleic acid extracts of cells, or biological fluids.
• the samples used in the above-described methods will vary based on the assay format, the detection method and the nature of the tissues, cells or extracts to be assayed. Methods for preparing nucleic acid extracts of cells are well known in the art and can be readily adapted in order to obtain a sample that is compatible with the method utilized.
• the present invention relates to an antibody having binding affinity to a kinase of the invention.
• the polypeptide may have the amino acid sequence selected from the group consisting of those set forth in SEQ ID NO:3 or 4 , or a functional derivative thereof, or at least 9 contiguous amino acids thereof (preferably, at least 20, 30, 35, or 40 contiguous amino acids thereof).
• the present invention also relates to an antibody having specific binding affinity to a kinase of the invention.
• an antibody may be isolated by comparing its binding affinity to a kinase of the invention with its binding affinity to other polypeptides.
• Those which bind selectively to a kinase of the invention would be chosen for use in methods requiring a distinction between a kinase of the invention and other polypeptides.
• Such methods could include, but should not be limited to, the analysis of altered kinase expression in tissue containing other polypeptides.
• the kinases of the present invention can be used in a variety of procedures and methods, such as for the generation of antibodies, for use in identifying pharmaceutical compositions, and for studying DNA/protein interaction.
• the kinases of the present invention can be used to produce antibodies or hybridomas.
• antibodies of the present invention include monoclonal and polyclonal antibodies, as well fragments of these antibodies, and humanized forms. Humanized forms of the antibodies of the present invention may be generated using one of the procedures known in the art such as chimerization or CDR grafting.
• the present invention also relates to a hybridoma which produces the above-described monoclonal antibody, or binding fragment thereof.
• a hybridoma is an immortalized cell line which is capable of secreting a specific monoclonal antibody.
• Any animal which is known to produce antibodies can be immunized with the selected polypeptide.
• Methods for immunization are well known in the art. Such methods include subcutaneous or intraperitoneal injection of the polypeptide.
• One skilled in the art will recognize that the amount of polypeptide used for immunization will vary based on the animal which is immunized, the antigenicity of the polypeptide and the site of injection.
• the polypeptide may be modified or administered in an adjuvant in order to increase the peptide antigenicity.
• Methods of increasing the antigenicity of a polypeptide are well known in the art. Such procedures include coupling the antigen with a heterologous protein (such as globulin or ⁇ -galactosidase) or through the inclusion of an adjuvant during immunization.
• a heterologous protein such as globulin or ⁇ -galactosidase
• spleen cells from the immunized animals are removed, fused with myeloma cells, such as SP2/0-Agl4 myeloma cells, and allowed to become monoclonal antibody producing hybridoma cells.
• myeloma cells such as SP2/0-Agl4 myeloma cells
• Any one of a number of methods well known in the art can be used to identify the hybridoma cell which produces an antibody with the desired characteristics. These include screening the hybridomas with an ELISA assay, western blot analysis, or radioimmunoassay (Lutz et al, Exp. Cell Res. 175:109-124, 1988).
• Hybridomas secreting the desired antibodies are cloned and the class and subclass are determined using procedures known in the art (Campbell, "Monoclonal Antibody
• antibody-containing antisera is isolated from the immunized animal and is screened for the presence of antibodies with the desired specificity using one of the above-described procedures.
• the above-described antibodies may be detectably labeled.
• Antibodies can be detectably labeled through the use of radioisotopes, affinity labels (such as biotin, avidin, and the like), enzymatic labels (such as horseradish peroxidase, alkaline phosphatase, and the like) fluorescent labels (such as FITC or rhodamine, and the like), paramagnetic atoms, and the like. Procedures for accomplishing such labeling are well-known in the art, for example, see Stemberger et al, J.
• the labeled antibodies of the present invention can be used for in vitro, in vivo, and in situ assays to identify cells or tissues which express a specific peptide.
• the above-described antibodies may also be immobilized on a solid support.
• solid supports include plastics such as polycarbonate, complex carbohydrates such as agarose and sepharose, acrylic resins such as polyacrylamide and latex beads. Techniques for coupling antibodies to such solid supports are well known in the art (Weir et al, "Handbook of Experimental Immunology” 4th Ed., Blackwell Scientific Publications, Oxford, England, Chapter 10, 1986; Jacoby et al, Meth. Enzym. 34, Academic Press, N.Y., 1974).
• the immobilized antibodies of the present invention can be used for in vitro, in vivo, and in situ assays as well as in immunochromotography.
• Anti-peptide peptides can be generated by replacing the basic amino acid residues found in the peptide sequences of the kinases of the invention with acidic residues, while maintaining hydrophobic and uncharged polar groups. For example, lysine, arginine, and/or histidine residues are replaced with aspartic acid or glutamic acid and glutamic acid residues are replaced by lysine, arginine or histidine.
• the present invention also encompasses a method of detecting a kinase polypeptide in a sample, comprising: (a) contacting the sample with an above-described antibody, under conditions such that immunocomplexes form, and (b) detecting the presence of said antibody bound to the polypeptide.
• the methods comprise incubating a test sample with one or more of the antibodies of the present invention and assaying whether the antibody binds to the test sample. Altered levels of a kinase of the invention in a sample as compared to normal levels may indicate disease.
• Incubation conditions vary. Incubation conditions depend on the format employed in the assay, the detection methods employed, and the type and nature of the antibody used in the assay.
• immunological assay formats such as radioimmunoassays, enzyme-linked immunosorbent assays, diffusion-based Ouchterlony, or rocket immunofluorescent assays
• Examples of such assays can be found in Chard ("An Introduction to Radioimmunoassay and Related Techniques" Elsevier Science Publishers, Amsterdam, The Netherlands, 1986), Bullock et al.
• the immunological assay test samples of the present invention include cells, protein or membrane extracts of cells, or biological fluids such as blood, serum, plasma, or urine.
• the test samples used in the above-described method will vary based on the assay format, nature of the detection method and the tissues, cells or extracts used as the sample to be assayed. Methods for preparing protein extracts or membrane extracts of cells are well known in the art and can readily be adapted in order to obtain a sample which is testable with the system utilized.
• kits contains all the necessary reagents to carry out the previously described methods of detection.
• the kit may comprise: (i) a first container means containing an above-described antibody, and (ii) second container means containing a conjugate comprising a binding partner of the antibody and a label.
• the kit further comprises one or more other containers comprising one or more of the following: wash reagents and reagents capable of detecting the presence of bound antibodies.
• detection reagents include, but are not limited to, labeled secondary antibodies, or in the alternative, if the primary antibody is labeled, the chromophoric, enzymatic, or antibody binding reagents which are capable of reacting with the labeled antibody.
• the compartmentalized kit may be as described above for nucleic acid probe kits.
• the antibodies described in the present invention can readily be inco ⁇ orated into one of the established kit formats which are well known in the art.
• the present invention also relates to a method of detecting a compound capable of binding to a kinase of the invention comprising incubating the compound with a kinase of the invention and detecting the presence of the compound bound to the kinase.
• the compound may be present within a complex mixture, for example, serum, body fluid, or cell extracts.
• the present invention also relates to a method of detecting an agonist or antagonist of kinase activity or kinase binding partner activity comprising incubating cells that produce a kinase of the invention in the presence of a compound and detecting changes in the level of kinase activity or kinase binding partner activity.
• the compounds thus identified would produce a change in activity indicative of the presence of the compound.
• the compound may be present within a complex mixture, for example, serum, body fluid, or cell extracts. Once the compound is identified it can be isolated using techniques well known in the art.
• the invention additionally provides methods for treating a disease or abnormal condition by administering to a patient in need of such treatment a substance that modulates the activity of a polypeptide selected from the group consisting of SEQ ID NO:3 and 4.
• the disease is selected from the group consisting of rheumatoid arthritis, atherosclerosis, autoimmune disorders, organ transplantation, myocardial infarction, cardiomyopathies, stroke, renal failure, oxidative stress-related neurodegenerative disorders, metabolic and reproductive disorders, and cancer.
• Substances useful for treatment of disorders or diseases preferably show positive results in one or more assays for an activity corresponding to treatment of the disease or disorder in question
• Substances that modulate the activity of the polypeptides preferably include, but are not limited to, antisense oligonucleotides and inhibitors of protein kinases.
• the term "preventing" refers to decreasing the probability that an organism contracts or develops an abnormal condition.
• treating refers to having a therapeutic effect and at least partially alleviating or abrogating an abnormal condition in the organism.
• a therapeutic effect refers to the inhibition or activation factors causing or contributing to the abnormal condition.
• a therapeutic effect relieves to some extent one or more of the symptoms of the abnormal condition.
• a therapeutic effect can refer to one or more of the following: (a) an increase in the proliferation, growth, and/or differentiation of cells; (b) inhibition (, slowing or stopping) of cell death; (c) inhibition of degeneration; (d) relieving to some extent one or more of the symptoms associated with the abnormal condition; and (e) enhancing the function of the affected population of cells.
• Compounds demonstrating efficacy against abnormal conditions can be identified as described herein.
• abnormal condition refers to a function in the cells or tissues of an organism that deviates from their normal functions in that organism.
• An abnormal condition can relate to cell proliferation, cell differentiation or cell survival.
• An abnormal condition may also include irregularities in cell cycle progression, i.e., irregularities in normal cell cycle progression through mitosis and meiosis.
• Abnormal cell proliferative conditions include cancers such as fibrotic and mesangial disorders, abnormal angiogenesis and vasculogenesis, wound healing, psoriasis, diabetes mellitus, and inflammation.
• Abnormal differentiation conditions include, but are not limited to, neurodegenerative disorders, slow wound healing rates, and slow tissue grafting healing rates.
• Abnormal cell survival conditions may also relate to conditions in which programmed cell death (apoptosis) pathways are activated or abrogated.
• apoptosis programmed cell death
• a number of protein kinases are associated with the apoptosis pathways. Aberrations in the function of any one of the protein kinases could lead to cell immortality or premature cell death.
• administering relates to a method of inco ⁇ orating a compound into cells or tissues of an organism. The abnormal condition can be prevented or treated when the cells or tissues of the organism exist within the organism or outside of the organism.
• Cells existing outside the organism can be maintained or grown in cell culture dishes.
• many techniques exist in the art to administer compounds including (but not limited to) oral, parenteral, dermal, injection, and aerosol applications.
• multiple techniques exist in the art to administer the compounds including (but not limited to) cell microinjection techniques, transformation techniques and carrier techniques.
• the abnormal condition can also be prevented or treated by administering a compound to a group of cells having an aberration in a signal transduction pathway to an organism.
• the effect of administering a compound on organism function can then be monitored.
• the organism is preferably a mouse, rat, rabbit, guinea pig or goat, more preferably a monkey or ape, and most preferably a human.
• the present invention also encompasses a method of agonizing (stimulating) or antagonizing kinase associated activity in a mammal comprising administering to said mammal an agonist or antagonist to a kinase of the invention in an amount sufficient to effect said agonism or antagonism.
• a method of treating diseases in a mammal with an agonist or antagonist of the activity of one of the kinases of the invention comprising .admimstering the agonist or antagonist to a mammal in an amount sufficient to agonize or antagonize kinase- associated functions is also encompassed in the present application.
• indolinone compounds form classes of acid resistant and membrane permeable organic molecules.
• WO 96/22976 published August 1, 1996 by Ballinari et al. describes hydrosoluble indolinone compounds that harbor tetralin, naphthalene, quinoline, and indole substituents fused to the oxindole ring. These bicyclic substituents are in turn substituted with polar moieties including hydroxylated alkyl, phosphate, and ether moieties.
• U.S. Patent Application Serial Nos. 08/702,232 filed August 23, 1996, entitled "Indolinone Combinatorial Libraries and Related Products and Methods for the Treatment of Disease" by Tang et al. (Lyon & Lyon Docket No.
• substances capable of modulating kinase activity include, but are not limited to, ty ⁇ hostins, quinazolines, quinoxolines, and quinolines.
• the quinazolines, ty ⁇ hostins, quinolines, and quinoxolines referred to above include well known compounds such as those described in the literature.
• representative publications describing quinazolines include Barker et al, EPO Publication No. 0 520 722 Al; Jones et al, U.S. Patent No. 4,447,608; Kabbe et al, U.S. Patent No. 4,757,072; Kaul and Vougioukas, U.S. Patent No. 5,316,553; Kreighbaum and Comer, U.S. Patent No. 4,343,940; Pegg and
• Ty ⁇ hostins are described in Allen et al, (1993) Clin. Exp. Immunol. 91:141-156; Anafi et al, (1993) Blood 82:12, 3524-3529; Baker et al, (1992) J. Cell Sci. 102:543-555; Bilder et al, (1991) Amer. Physiol. Soc. pp. 6363-6143:C721-C730; Brunton et al, (1992) Proceedings of Amer. Assoc. Cancer Rsch. 33:558; Bryckaert et al, (1992) Exp. Cell Research 199:255-261; Dong et al, (1993) J.
• oxindolinones such as those described in U.S. patent application Serial No. 08/702,232 filed August 23, 1996, inco ⁇ orated herein by reference in its entirety, including any drawings.
• the present invention also relates to a recombinant DNA molecule comprising, 5' to 3', a promoter effective to initiate transcription in a host cell and the above-described nucleic acid molecules.
• the present invention relates to a recombinant DNA molecule comprising a vector and an above-described nucleic acid molecule.
• the present invention also relates to a nucleic acid molecule comprising a transcriptional region functional in a cell, a sequence complementary to an RNA sequence encoding an amino acid sequence corresponding to the above-described polypeptide, and a transcriptional termination region functional in said cell.
• the above-described molecules may be isolated and/or purified DNA molecules.
• the present invention also relates to a cell or organism that contains an above- described nucleic acid molecule and thereby is capable of expressing a polypeptide.
• the polypeptide may be purified from cells which have been altered to express the polypeptide.
• a cell is said to be "altered to express a desired polypeptide" when the cell, through genetic manipulation, is made to produce a protein which it normally does not produce or which the cell normally produces at lower levels.
• One skilled in the art can readily adapt procedures for introducing and expressing either genomic, cDNA, or synthetic sequences into either eukaryotic or prokaryotic cells.
• a nucleic acid molecule such as DNA, is said to be "capable of expressing" a polypeptide if it contains nucleotide sequences which contain transcriptional and translational regulatory information and such sequences are “operably linked” to nucleotide sequences which encode the polypeptide.
• An operable linkage is a linkage in which the regulatory DNA sequences and the DNA sequence sought to be expressed are connected in such a way as to permit gene sequence expression.
• the precise nature of the regulatory regions needed for gene sequence expression may vary from organism to organism, but shall in general include a promoter region which, in prokaryotes, contains both the promoter (which directs the initiation of RNA transcription) as well as the DNA sequences which, when transcribed into RNA, will signal synthesis initiation. Such regions will normally include those 5'-non-coding sequences involved with initiation of transcription and translation, such as the TATA box, capping sequence, CAAT sequence, and the like.
• the non-coding region 3' to the sequence encoding a kinase of the invention may be obtained by the above-described methods.
• This region may be retained for its transcriptional termination regulatory sequences, such as termination and polyadenylation.
• the transcriptional termination signals may be provided. Where the transcriptional termination signals are not satisfactorily functional in the expression host cell, then a 3' region functional in the host cell may be substituted.
• Two DNA sequences are said to be operably linked if the nature of the linkage between the two DNA sequences does not (1) result in the introduction of a frame-shift mutation, (2) interfere with the ability of the promoter region sequence to direct the transcription of a gene sequence encoding a kinase of the invention, or (3) interfere with the ability of the gene sequence of a kinase of the invention to be transcribed by the promoter region sequence.
• a promoter region would be operably linked to a DNA sequence if the promoter were capable of effecting transcription of that DNA sequence.
• the present invention encompasses the expression of a gene encoding a kinase of the invention (or a functional derivative thereof) in either prokaryotic or eukaryotic cells.
• Prokaryotic hosts are, generally, very efficient and convenient for the production of recombinant proteins and are, therefore, one type of preferred expression system for kinases of the invention.
• Prokaryotes most frequently are represented by various strains of E. coli. However, other microbial strains may also be used, including other bacterial strains.
• plasmid vectors that contain replication sites and control sequences derived from a species compatible with the host may be used.
• suitable plasmid vectors may include pBR322, pUCl 18, pUCl 19 and the like; suitable phage or bacteriophage vectors may include ⁇ gtlO, ⁇ gtl 1 and the like; and suitable virus vectors may include pMAM-neo, pKRC and the like.
• the selected vector of the present invention has the capacity to replicate in the selected host cell. Recognized prokaryotic hosts include bacteria such as E. coli, Bacillus, Streptomyces,
• the prokaryotic host must be compatible with the replicon and control sequences in the expression plasmid.
• a kinase of the invention (or a functional derivative thereof) in a prokaryotic cell, it is necessary to operably link the sequence encoding the kinase of the invention to a functional prokaryotic promoter.
• promoters may be either constitutive or, more preferably, regulatable (i.e., inducible or derepressible).
• constitutive promoters include the int promoter of bacteriophage ⁇ , the bla promoter of the ⁇ -lactamase gene sequence of pBR322, and the cat promoter of the chloramphenicol acetyl transferase gene sequence of pPR325, and the like.
• inducible prokaryotic promoters examples include the major right and left promoters of bacteriophage ⁇ (P L and P R ), the trp, ⁇ recA, acZ, ⁇ acl, and gal promoters of E. coli, the ⁇ -amylase (Ulmanen et al, J. Bacteriol 162: 176-182, 1985) and the ⁇ -28-specific promoters of B.
• subtilis (Gilman et al, Gene Sequence 32:11-20, 1984), the promoters of the bacteriophages of Bacillus (Gryczan, in: The Molecular Biology of the Bacilli, Academic Press, Inc., NY, 1982), and Streptomyces promoters (Ward et al, Mol. Gen. Genet. 203:468-478, 1986).
• Prokaryotic promoters are reviewed by Glick (In d. Microbiot. 1:277-282, 1987), Cenatiempo (Biochimie 68:505-516, 1986), and Gottesman (Ann. Rev. Genet. 18:415-442, 1984).
• progeny Proper expression in a prokaryotic cell also requires the presence of a ribosome- binding site upstream of the gene sequence-encoding sequence.
• ribosome-binding sites are disclosed, for example, by Gold et al. (Ann. Rev. Microbiol. 35:365-404, 1981).
• the selection of control sequences, expression vectors, transformation methods, and the like, are dependent on the type of host cell used to express the gene.
• “cell”, “cell line”, and “cell culture” may be used interchangeably and all such designations include progeny.
• the words “fransformants” or “transformed cells” include the primary subject cell and cultures derived therefrom, without regard to the number of transfers. It is also understood that all progeny may not be precisely identical in DNA content, due to deliberate or inadvertent mutations. However, as defined, mutant progeny have the same functionality as that of the originally transformed cell.
• Host cells which may be used in the expression systems of the present invention are not strictly limited, provided that they are suitable for use in the expression of the kinase polypeptide of interest. Suitable hosts may often include eukaryotic cells. Preferred eukaryotic hosts include, for example, yeast, fungi, insect cells, mammalian cells either in vivo, or in tissue culture. Mammalian cells which may be useful as hosts include HeLa cells, cells of fibroblast origin such as VERO or CHO-K1, or cells of lymphoid origin and their derivatives. Preferred mammalian host cells include SP2/0 and J558L, as well as neuroblastoma cell lines such as IMR 332, which may provide better capacities for correct post-franslational processing.
• plant cells are also available as hosts, and control sequences compatible with plant cells are available, such as the cauliflower mosaic virus 35S and 19S, and nopaline synthase promoter and polyadenylation signal sequences.
• Another preferred host is an insect cell, for example the Drosophila larvae. Using insect cells as hosts, the Drosophila alcohol dehydrogenase promoter can be used (Rubin, Science 240:1453-1459, 1988).
• baculovirus vectors can be engineered to express large amounts of kinases of the invention in insect cells (Jasny, Science 238:1653, 1987; Miller et al, in: Genetic Engineering, Vol. 8, Plenum, Setlow et al, eds., pp.
• yeast expression systems Any of a series of yeast expression systems can be utilized which inco ⁇ orate promoter and termination elements from the actively expressed sequences coding for glycolytic enzymes that are produced in large quantities when yeast are grown in mediums rich in glucose. Known glycolytic gene sequences can also provide very efficient transcriptional control signals. Yeast provides substantial advantages in that it can also carry out post-franslational modifications. A number of recombinant DNA strategies exist utilizing strong promoter sequences and high copy number plasmids which can be utilized for production of the desired proteins in yeast. Yeast recognizes leader sequences on cloned mammalian genes and secretes peptides bearing leader sequences (i.e., pre-peptides). Several possible vector systems are available for the expression of kinases of the invention in a mammalian host.
• transcriptional and translational regulatory sequences may be employed, depending upon the nature of the host.
• the transcriptional and translational regulatory signals may be derived from viral sources, such as adenovirus, bovine papilloma virus, cytomegalovirus, simian virus, or the like, where the regulatory signals are associated with a particular gene sequence which has a high level of expression.
• promoters from mammalian expression products such as actin, collagen, myosin, and the like, may be employed.
• Transcriptional initiation regulatory signals may be selected which allow for repression or activation, so that expression of the gene sequences can be modulated.
• kinases of the invention in eukaryotic hosts requires the use of eukaryotic regulatory regions. Such regions will, in general, include a promoter region sufficient to direct the initiation of RNA synthesis.
• Preferred eukaryotic promoters include, for example, the promoter of the mouse metallothionein I gene sequence (Hamer et al, J. Mol. Appl. Gen.
• a nucleic acid molecule encoding a kinase of the invention and an operably linked promoter may be introduced into a recipient prokaryotic or eukaryotic cell either as a nonreplicating D ⁇ A or R ⁇ A molecule, which may either be a linear molecule or, more preferably, a closed covalent circular molecule. Since such molecules are incapable of autonomous replication, the expression of the gene may occur through the transient expression of the introduced sequence. Alternatively, permanent expression may occur through the integration of the introduced D ⁇ A sequence into the host chromosome.
• a vector may be employed which is capable of integrating the desired gene sequences into the host cell chromosome.
• Cells which have stably integrated the introduced DNA into their chromosomes can be selected by also introducing one or more markers which allow for selection of host cells which contain the expression vector.
• the marker may provide for protofrophy to an auxofrophic host, biocide resistance, e.g., antibiotics, or heavy metals, such as copper, or the like.
• the selectable marker gene sequence can either be directly linked to the DNA gene sequences to be expressed, or introduced into the same cell by co-transfection. Additional elements may also be needed for optimal synthesis of mRNA. These elements may include splice signals, as well as transcription promoters, enhancers, and termination signals. cDNA expression vectors inco ⁇ orating such elements include those described by Okayama (Mol. Cell. Biol. 3:280-289, 1983).
• the introduced nucleic acid molecule can be inco ⁇ orated into a plasmid or viral vector capable of autonomous replication in the recipient host.
• a plasmid or viral vector capable of autonomous replication in the recipient host.
• Any of a wide variety of vectors may be employed for this pu ⁇ ose. Factors of importance in selecting a particular plasmid or viral vector include: the ease with which recipient cells that contain the vector may be recognized and selected from those recipient cells which do not contain the vector; the number of copies of the vector which are desired in a particular host; and whether it is desirable to be able to "shuttle" the vector between host cells of different species.
• Preferred prokaryotic vectors include plasmids such as those capable of replication in E. coli (such as, for example, ⁇ BR322, Col ⁇ l, pSClOl, pACYC 184, ⁇ VX; "Molecular Cloning: A Laboratory Manual", 1989, supra).
• Bacillus plasmids include pC194, pC221, pT127, and the like (Gryczan, In: The Molecular Biology of the Bacilli, Academic Press, NY, pp. 307-329, 1982).
• Suitable Streptomyces plasmids include plJlOl (Kendall et al, J.
• Preferred eukaryotic plasmids include, for example, BPV, vaccinia, SV40, 2-micron circle, and the like, or their derivatives.
• Such plasmids are well known in the art (Botstein et al, Miami Wnfr. Symp. 19:265-274, 1982; Broach, In: "The Molecular Biology of the Yeast Saccharomyces: Life Cycle and Inheritance", Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, p. 445-470, 1981; Broach, Cell 28:203-204, 1982; Bollon et al, J. Clin. Hematol. Oncol. 10:39-48, 1980; Maniatis, h : Cell Biology: A Comprehensive Treatise, Vol. 3, Gene Sequence Expression, Academic Press, NY, pp. 563-608, 1980).
• the DNA construct(s) may be introduced into an appropriate host cell by any of a variety of suitable means, i.e. , transformation, transfection, conjugation, protoplast fusion, electroporation, particle gun technology, calcium phosphate-precipitation, direct microinjection, and the like.
• recipient cells are grown in a selective medium, which selects for the growth of vector-containing cells. Expression of the cloned gene(s) results in the production of a kinase of the invention, or fragments thereof.
• DNA can be injected into the pronucleus of a fertilized egg before fusion of the male and female pronuclei, or injected into the nucleus of an embryonic cell (e.g. , the nucleus of a two-cell embryo) following the initiation of cell division (Brinster et al, Proc. Nat. Acad. Sci. USA 82:4438-4442, 1985).
• Embryos can be infected with viruses, especially retroviruses, modified to carry inorganic-ion receptor nucleotide sequences of the invention.
• Pluripotent stem cells derived from the inner cell mass of the embryo and stabilized in culture can be manipulated in culture to inco ⁇ orate nucleotide sequences of the invention.
• a transgenic animal can be produced from such cells through implantation into a blastocyst that is implanted into a foster mother and allowed to come to term. Animals suitable for transgenic experiments can be obtained from standard commercial sources such as Charles River (Wilmington, MA), Taconic (Germantown, NY), Harlan Sprague Dawley (Indianapolis, IN), etc.
• transgenic mouse female mice are induced to superovulate. Females are placed with males, and the mated females are sacrificed by CO 2 asphyxiation or cervical dislocation and embryos are recovered from excised oviducts. Surrounding cumulus cells are removed. Pronuclear embryos are then washed and stored until the time of injection. Randomly cycling adult female mice are paired with vasectomized males. Recipient females are mated at the same time as donor females. Embryos then are transferred surgically. The procedure for generating transgenic rats is similar to that of mice (Hammer et al, Cell 63:1099-1112, 1990).
• a clone containing the sequence(s) of the invention is co-transfected with a gene encoding resistance.
• the gene encoding neomycin resistance is physically linked to the sequence(s) of the invention.
• DNA molecules introduced into ES cells can also be integrated into the chromosome through the process of homologous recombina-tion (Capecchi, Science 244:1288-1292, 1989).
• Methods for positive selection of the recombination event (i.e., neo resistance) and dual positive-negative selection (i.e. , neo resistance and gancyclovir resistance) and the subsequent identification of the desired clones by PCR have been described by Capecchi, supra and Joyner et al (Nature 338:153-156, 1989), the teachings of which are inco ⁇ orated herein in their entirety including any drawings.
• the final phase of the procedure is to inject targeted ES cells into blastocysts and to transfer the blastocysts into pseudopregnant females.
• the resulting chimeric animals are bred and the offspring are analyzed by Southern blotting to identify individuals that carry the transgene.
• Procedures for the production of non-rodent mammals and other animals have been discussed by others (Houdebine and Chourrout, supra; Pursel et al, Science 244:1281-1288, 1989; and Simms et al, Bio/Technology 6:179- 183, 1988).
• the invention provides transgenic, nonhuman mammals containing a transgene encoding a kinase of the invention or a gene affecting the expression of the kinase.
• Such transgenic nonhuman mammals are particularly useful as an in vivo test system for studying the effects of introduction of a kinase, or regulating the expression of a kinase (i.e., through the introduction of additional genes, antisense nucleic acids, or ribozymes).
• transgenic animal is an animal having cells that contain DNA which has been artificially inserted into a cell, which DNA becomes part of the genome of the animal which develops from that cell.
• Preferred transgenic animals are primates, mice, rats, cows, pigs, horses, goats, sheep, dogs and cats.
• the transgenic DNA may encode human kinases. Native expression in an animal may be reduced by providing an amount of antisense RNA or DNA effective to reduce expression of the receptor.
• an expression vector containing a kinase coding sequence is inserted into cells, the cells are grown in vitro and then infused in large numbers into patients.
• a DNA segment containing a promoter of choice (for example a strong promoter) is transferred into cells containing an endogenous gene encoding kinases of the invention in such a manner that the promoter segment enhances expression of the endogenous kinase gene (for example, the promoter segment is transferred to the cell such that it becomes directly linked to the endogenous kinase gene).
• the gene therapy may involve the use of an adenovirus containing kinase cDNA targeted to a tumor, systemic kinase increase by implantation of engineered cells, injection with kinase-encoding virus, or injection of naked kinase DNA into appropriate tissues.
• Target cell populations may be modified by introducing altered forms of one or more components of the protein complexes in order to modulate the activity of such complexes. For example, by reducing or inhibiting a complex component activity within target cells, an abnormal signal transduction event(s) leading to a condition may be decreased, inhibited, or reversed. Deletion or missense mutants of a component, that retain the ability to interact with other components of the protein complexes but cannot function in signal transduction, may be used to inhibit an abnormal, deleterious signal transduction event.
• Expression vectors derived from viruses such as retroviruses, vaccinia virus, adenovirus, adeno-associ-ated virus, he ⁇ es viruses, several RNA viruses, or bovine papilloma virus, may be used for delivery of nucleotide sequences (e.g., cDNA) encod-ing recom-binant kinase of the invention protein into the targeted cell population (e.g., tumor cells).
• viruses such as retroviruses, vaccinia virus, adenovirus, adeno-associ-ated virus, he ⁇ es viruses, several RNA viruses, or bovine papilloma virus.
• recombinant viral vectors contain-ing coding sequences (Maniatis et al, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, N.Y., 1989; Ausubel et al, Current Proto-cols in Molecular Biology, Greene Publishing Associates and Wiley Interscience, N.Y., 1989).
• recombinant nucleic acid mole-cules encoding protein sequences can be used as naked DNA or in a recon-stituted system e.g., lipo-somes or other lipid systems for delivery to target cells (e.g., Feigner et al, Nature 337:387-8, 1989).
• Several other methods for the direct transfer of plasmid DNA into cells exist for use in human gene therapy and involve targeting the DNA to receptors on cells by complexing the plasmid DNA to proteins (Miller, supra).
• gene transfer can be performed by simply injecting minute amounts of DNA into the nucleus of a cell, through a process of microinjection (Capecchi, Cell 22:479-88, 1980). Once recombinant genes are introduced into a cell, they can be recognized by the cell's normal mechanisms for transcription and translation, and a gene product will be expressed. Other methods have also been attempted for introducing DNA into larger numbers of cells. These methods include: transfection, wherein DNA is precipitated with calcium phosphate and taken into cells by pinocytosis (Chen et al, Mol. Cell Biol.
• adenovirus proteins are capable of destabilizing endosomes and enhancing the uptake of DNA into cells.
• the admixture of adenovirus to solutions containing DNA complexes, or the binding of DNA to polylysine covalently attached to adenovirus using protein crosslinking agents substantially improves the uptake and expression of the recombinant gene (Curiel et al, Am. J. Respir. Cell. Mol. Biol, 6:247- 52, 1992).
• Gene transfer means the process of introducing a foreign nucleic acid molecule into a cell. Gene transfer is commonly performed to enable the expres-sion of a particular product encoded by the gene.
• the product may include a protein, polypeptide, anti-sense DNA or RNA, or enzymatically active RNA.
• Gene transfer can be performed in cultured cells or by direct administration into animals. Generally gene transfer involves the process of nucleic acid contact with a target cell by non-specific or receptor mediated interactions, uptake of nucleic acid into the cell through the membrane or by endocytosis, and release of nucleic acid into the cyto-plasm from the plasma membrane or endosome. Expression may require, in addition, movement of the nucleic acid into the nucleus of the cell and binding to appropriate nuclear factors for transcription.
• gene therapy is a form of gene transfer and is included within the definition of gene transfer as used herein and specifically refers to gene transfer to express a therapeutic product from a cell in vivo or in vitro. Gene transfer can be performed ex vivo on cells which are then transplanted into a patient, or can be performed by direct admimstration of the nucleic acid or nucleic acid-protein complex into the patient.
• a vector having nucleic acid sequences encoding a kinase polypeptide in which the nucleic acid sequence is expressed only in specific tissue.
• Methods of achieving tissue-specific gene expression are set forth in International Publication No. WO 93/09236, filed November 3, 1992 and published May 13, 1993.
• nucleic acid sequence contained in the vector may include additions, deletions or modifications to some or all of the sequence of the nucleic acid, as defined above.
• a method of gene replacement is set forth. "Gene replacement" as used herein means supplying a nucleic acid sequence which is capable of being expressed in vivo in an animal and thereby providing or augmenting the function of an endogenous gene which is missing or defective in the animal.
• the compounds described herein can be administered to a human patient per se, or in pharmaceutical compositions where it is mixed with other active ingredients, as in combination therapy, or suitable carriers or excipient(s).
• suitable carriers or excipient(s) suitable carriers or excipient(s).
• Suitable routes of administration may, for example, include oral, rectal, transmucosal, or intestinal administration; parenteral delivery, including intramuscular, subcutaneous, intravenous, intramedullary injections, as well as intrathecal, direct intraventricular, intraperitoneal, intranasal, or intraocular injections.
• the liposomes will be targeted to and taken up selectively by the tumor.
• compositions of the present invention may be manufactured in a manner that is itself known, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or lyophilizing processes.
• Pharmaceutical compositions for use in accordance with the present invention thus may be formulated in conventional manner using one or more physiologically acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. Proper formulation is dependent upon the route of administration chosen.
• the agents of the invention may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks's solution, Ringer's solution, or physiological saline buffer.
• penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.
• the compounds can be formulated readily by combining the active compounds with pharmaceutically acceptable carriers well known in the art.
• Such carriers enable the compounds of the invention to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a patient to be treated.
• Suitable carriers include excipients such as, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropyhnethyl- cellulose, sodium carboxymethylcellulose, and/or polyvinylpyrrolidone (PVP).
• disintegrating agents may be added, such as the cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.
• Dragee cores are provided with suitable coatings.
• suitable coatings For this pu ⁇ ose, concentrated sugar solutions may be used, which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures.
• Dyestuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.
• compositions which can be used orally include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol.
• the push-fit capsules can contain the active ingredients in admixture with filler such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers.
• the active compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols.
• stabilizers may be added. All formulations for oral administration should be in dosages suitable for such administration.
• the compositions may take the form of tablets or lozenges formulated in conventional manner.
• the compounds for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebuliser, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroetha ⁇ e, carbon dioxide or other suitable gas.
• a suitable propellant e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroetha ⁇ e, carbon dioxide or other suitable gas.
• a suitable propellant e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroetha ⁇ e, carbon dioxide or other suitable gas.
• the dosage unit may be determined by providing a valve to deliver a metered amount.
• the compounds may be formulated for parenteral administration by injection, e.g., by bolus injection or continuous infusion.
• Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multi-dose containers, with an added preservative.
• the compositions may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.
• Pharmaceutical formulations for parenteral admimstration include aqueous solutions of the active compounds in water-soluble form. Additionally, suspensions of the active compounds may be prepared as appropriate oily injection suspensions.
• Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes.
• Aqueous injection suspensions may contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran.
• the suspension may also contain suitable stabilizers or agents which increase the solubility of the compounds to allow for the preparation of highly concentrated solutions.
• the active ingredient may be in powder form for constitution with a suitable vehicle, e.g. , sterile pyrogen-free water, before use.
• a suitable vehicle e.g. , sterile pyrogen-free water
• the compounds may also be formulated in rectal compositions such as suppositories or retention enemas, e.g., containing conventional suppository bases such as cocoa butter or other glycerides.
• the compounds may also be formulated as a depot preparation. Such long acting formulations may be administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection.
• the compounds may be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.
• a pharmaceutical carrier for the hydrophobic compounds of the invention is a cosolvent system comprising benzyl alcohol, a nonpolar surfactant, a water-miscible organic polymer, and an aqueous phase.
• the cosolvent system may be the VPD co-solvent system.
• VPD is a solution of 3% w/v benzyl alcohol, 8% w/v of the nonpolar surfactant polysorbate 80, and 65% w/v polyethylene glycol 300, made up to volume in absolute ethanol.
• the VPD co-solvent system (VPD:D5W) consists of VPD diluted 1:1 with a 5% dextrose in water solution. This co-solvent system dissolves hydrophobic compounds well, and itself produces low toxicity upon systemic administration.
• co-solvent system may be varied considerably without destroying its solubility and toxicity characteristics.
• identity of the co-solvent components may be varied: for example, other low-toxicity nonpolar surfactants may be used instead of polysorbate 80; the fraction size of polyethylene glycol may be varied; other biocompatible polymers may replace polyethylene glycol, e.g. polyvinyl pyrrolidone; and other sugars or polysaccharides may substitute for dextrose.
• hydrophobic pharmaceutical compounds may be employed.
• Liposomes and emulsions are well known examples of delivery vehicles or carriers for hydrophobic drugs.
• Certain organic solvents such as dimethylsulfoxide also may be employed, although usually at the cost of greater toxicity.
• the compounds may be delivered using a sustained-release system, such as semipermeable matrices of solid hydrophobic polymers containing the therapeutic agent.
• sustained-release materials have been established and are well known by those skilled in the art. Sustained-release capsules may, depending on their chemical nature, release the compounds for a few weeks up to over 100 days.
• additional strategies for protein stabilization may be employed.
• compositions also may comprise suitable solid or gel phase carriers or excipients.
• suitable solid or gel phase carriers or excipients include but are not limited to calcium carbonate, calcium phosphate, various sugars, starches, cellulose derivatives, gelatin, and polymers such as polyethylene glycols.
• Many of the tyrosine or serine/threonine kinase modulating compounds of the invention may be provided as salts with pharmaceutically compatible counterions.
• Pharmaceutically compatible salts may be formed with many acids, including but not limited to hydrochloric, sulfuric, acetic, lactic, tartaric, malic, succinic, etc. Salts tend to be more soluble in aqueous or other protonic solvents that are the corresponding free base forms.
• compositions suitable for use in the present invention include compositions where the active ingredients are contained in an amount effective to achieve its intended pu ⁇ ose. More specifically, a therapeutically effective amount means an amount of compound effective to prevent, alleviate or ameliorate symptoms of disease or prolong the survival of the subject being treated. Determination of a therapeutically effective amount is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein. Methods of determining the dosages of compounds to be administered to a patient and modes of administering compounds to an organism are disclosed in U.S. Application Serial No. 08/702,282, filed August 23, 1996 and International patent publication number WO 96/22976, published August 1 1996, both of which are inco ⁇ orated herein by reference in their entirety, including any drawings, figures or tables. Those skilled in the art will appreciate that such descriptions are applicable to the present invention and can be easily adapted to it.
• Therapeutically effective doses for the compounds described herein can be estimated initially from cell culture and animal models. For example, a dose can be formulated in animal models to achieve a circulating concentration range that initially takes into account the IC 50 as determined in cell culture assays. The animal model data can be used to more accurately determine useful doses in humans.
• the therapeutically effective dose can be estimated imtially from cell culture assays.
• a dose can be formulated in animal models to achieve a circulating concentration range that includes the IC 5 o as determined in cell culture (i.e., the concentration of the test compound which achieves a half-maximal inhibition of the tyrosine or serine/threonine kinase activity).
• concentration range that includes the IC 5 o as determined in cell culture (i.e., the concentration of the test compound which achieves a half-maximal inhibition of the tyrosine or serine/threonine kinase activity).
• Toxicity and therapeutic efficacy of the compounds described herein can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED 50 (the dose therapeutically effective in 50%> of the population).
• the dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio between LD 50 and ED 5 o.
• Compounds which exhibit high therapeutic indices are preferred.
• the data obtained from these cell culture assays and animal studies can be used in formulating a range of dosage for use in human.
• the dosage of such compounds lies preferably within a range of circulating concentrations that include the ED 5 o with little or no toxicity.
• the dosage may vary within this range depending upon the dosage form employed and the route of administration utilized.
• the exact fonnulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. (See e.g., Fingl et al, 1975, in "The Pharmacological Basis of Therapeutics", Ch. 1 p.1).
• toxicity studies can be carried out by measuring the blood cell composition.
• toxicity studies can be carried out in a suitable animal model as follows: 1) the compound is administered to mice (an untreated control mouse should also be used); 2) blood samples are periodically obtained via the tail vein from one mouse in each treatment group; and 3) the samples are analyzed for red and white blood cell counts, blood cell composition and the percent of lymphocytes versus polymo ⁇ honuclear cells. A comparison of results for each dosing regime with the controls indicates if toxicity is present.
• Plasma half-life and biodistribution of the drug and metabolites in the plasma, tumors and major organs can also be determined to facilitate the selection of drugs most appropriate to inhibit a disorder. Such measurements can be carried out.
• HPLC analysis can be performed on the plasma of animals treated with the drug and the location of radiolabeled compounds can be determined using detection methods such as X-ray, CAT scan and MRI.
• detection methods such as X-ray, CAT scan and MRI.
• Compounds that show potent inhibitory activity in the screening assays, but have poor pharmacokinetic characteristics can be optimized by altering the chemical structure and retesting. In this regard, compounds displaying good pharmacokinetic characteristics can be used as a model.
• Dosage amount and interval may be adjusted individually to provide plasma levels of the active moiety which are sufficient to maintain the kinase modulating effects, or minimal effective concentration (MEC).
• MEC minimal effective concentration
• the MEC will vary for each compound but can be estimated from in vitro data; e.g., the concentration necessary to achieve 50-90%) inhibition of the kinase using the assays described herein. Dosages necessary to achieve the MEC will depend on individual characteristics and route of administration. However, HPLC assays or bioassays can be used to determine plasma concentrations.
• Dosage intervals can also be determined using MEC value.
• Compounds should be administered using a regimen which maintains plasma levels above the MEC for 10-90% of the time, preferably between 30-90% and most preferably between 50-90%.
• the effective local concentration of the drug may not be related to plasma concentration.
• composition administered will, of course, be dependent on the subject being treated, on the subject's weight, the severity of the affliction, the manner of administration and the judgment of the prescribing physician.
• compositions may, if desired, be presented in a pack or dispenser device which may contain one or more unit dosage forms containing the active ingredient.
• the pack may for example comprise metal or plastic foil, such as a blister pack.
• the pack or dispenser device may be accompanied by instructions for admimstration.
• the pack or dispenser may also be accompanied with a notice associated with the container in form prescribed by a governmental agency regulating the manufacture, use, or sale of pharmaceuticals, which notice is reflective of approval by the agency of the form of the polynucleotide for human or veterinary administration.
• Such notice for example, may be the labeling approved by the U.S. Food and Drug Administration for prescription drugs, or the approved product insert.
• compositions comprising a compound of the invention formulated in a compatible pharmaceutical carrier may also be prepared, placed in an appropriate container, and labeled for treatment of an indicated condition.
• Suitable conditions indicated on the label may include treatment of a tumor, inhibition of angiogenesis, treatment of fibrosis, diabetes, and the like.
• a functional derivative retains at least a portion of the function of the protein, for example reactivity with an antibody specific for the protein, enzymatic activity or binding activity mediated through noncatalytic domains, which permits its utility in accordance with the present invention. It is well known in the art that due to the degeneracy of the genetic code numerous different nucleic acid sequences can code for the same amino acid sequence.
• nucleic acid sequence significantly different from one selected from the group consisting of those set forth in SEQ ID NO:l and SEQ ID NO:2.
• the encoded amino acid sequence thereof would, however, be preserved.
• nucleic acid sequence may comprise a nucleotide sequence which results from the addition, deletion or substitution of at least one nucleotide to the 5'-end and/or the 3 '-end of the nucleic acid formula selected from the group consisting of those set forth in SEQ ID NO:l and SEQ ID NO:2, or a derivative thereof.
• nucleotide or polynucleotide may be used in this regard, provided that its addition, deletion or substitution does not alter the amino acid sequence of selected from the group consisting of those set forth in SEQ ID NO:l, and SEQ ID NO:2 which is encoded by the nucleotide sequence.
• the present invention is intended to include any nucleic acid sequence resulting from the addition of ATG as an initiation codon at the 5 '-end of the inventive nucleic acid sequence or its derivative, or from the addition of TTA, TAG or TGA as a termination codon at the 3 '-end of the inventive nucleotide sequence or its derivative.
• the nucleic acid molecule of the present invention may, as necessary, have restriction endonuclease recognition sites added to its 5'-end and/or 3'-end.
• nucleic acid sequence affords an opportunity to promote secretion and/or processing of heterologous proteins encoded by foreign nucleic acid sequences fused thereto.
• All variations of the nucleotide sequence of the kinase genes of the invention and fragments thereof permitted by the genetic code are, therefore, included in this invention.
• the two polypeptides are functionally equivalent, as are the two nucleic acid molecules that give rise to their production, even though the differences between the nucleic acid molecules are not related to the degeneracy of the genetic code.
• a "chemical derivative" of the complex contains additional chemical moieties not normally a part of the protein. Covalent modifications of the protein or peptides are included within the scope of this invention. Such modifications may be introduced into the molecule by reacting targeted amino acid residues of the peptide with an organic derivatizing agent that is capable of reacting with selected side chains or terminal residues, as described below.
• Cysteinyl residues most commonly are reacted with alpha-haloacetates (and corresponding amines), such as chloroacetic acid or chloroacetamide, to give carboxymethyl or carboxyamidomethyl derivatives. Cysteinyl residues also are derivatized by reaction with bromotrifluoroacetone, chloroacetyl phosphate, N-alkylmaleimides, 3-nitro-2-pyridyl disulfide, methyl 2-pyridyl disulfide, p-chloromercuribenzoate, 2-chloromercuri-4- nitrophenol, or chloro-7-nitrobenzo-2-oxa-l,3-diazole.
• Histidyl residues are derivatized by reaction with diethylprocarbonate at pH 5.5-7.0 because this agent is relatively specific for the histidyl side chain.
• Para-bromophenacyl bromide also is useful; the reaction is preferably performed in 0.1 M sodium cacodylate at pH 6.0.
• Lysinyl and amino terminal residues are reacted with succinic or other carboxylic acid anhydrides. Derivatization with these agents has the effect or reversing the charge of the lysinyl residues.
• Other suitable reagents for derivatizing primary amine containing residues include imidoesters such as methyl picolinimidate; pyridoxal phosphate; pyridoxal; chloroborohydri.de; trinitrobenzenesulfonic acid; O-methylisourea; 2,4 pentanedione; and transaminase-catalyzed reaction with glyoxylate.
• Arginyl residues are modified by reaction with one or several conventional reagents, among them phenylglyoxal, 2,3-butanedione, 1,2-cyclohexanedione, and ninhydrin. Derivatization of arginine residues requires that the reaction be performed in alkaline conditions because of the high pK a of the guanidine functional group. Furthermore, these reagents may react with the groups of lysine as well as the arginine alpha-amino group.
• Tyrosyl residues are well-known targets of modification for introduction of spectral labels by reaction with aromatic diazonium compounds or tetranitromethane. Most commonly, N-acetylimidizol and tetranitromethane are used to form O-acetyl tyrosyl species and 3-nitro derivatives, respectively.
• Carboxyl side groups are selectively modified by reaction with carbodiimide (R'-N-C-N-R') such as l-cyclohexyl-3-(2-mo ⁇ holinyl(4-ethyl) carbodiimide or l-ethyl-3-(4-azonia-4,4-dimethylpentyl) carbodiimide.
• carbodiimide R'-N-C-N-R'
• aspartyl and glutamyl residues are converted to asparaginyl and glutaminyl residues by reaction with ammonium ions.
• Glutaminyl and asparaginyl residues are frequently deamidated to the corresponding glutamyl and aspartyl residues. Alternatively, these residues are deamidated under mildly acidic conditions. Either form of these residues falls within the scope of this invention.
• Derivatization with bifunctional agents is useful, for example, for cross-linking the component peptides of the protein to each other or to other proteins in a complex to a water- insoluble support matrix or to other macromolecular carriers.
• Commonly used cross-linking agents include, for example, l,l-bis(diazoacetyl)-2-phenylethane, glutaraldehyde, N- hydroxysuccinimide esters, for example, esters with 4-azidosalicylic acid, homobifunctional imidoesters, including disuccinimidyl esters such as 3,3'-dithiobis(succinimidylpropionate), and bifunctional maleimides such as bis-N-maleimido-l,8-octane.
• Derivatizing agents such as methyl-3-[p-azidophenyl) dithiolpropioimidate yield photoactivatable intermediates that are capable of forming crosslinks in the presence of light.
• reactive water- insoluble matrices such as cyanogen bromide-activated carbohydrates and the reactive substrates described in U.S. Patent Nos. 3,969,287; 3,691,016; 4,195,128; 4,247,642; 4,229,537; and 4,330,440 are employed for protein immobilization.
• Such derivatized moieties may improve the stability, solubility, abso ⁇ tion, biological half life, and the like.
• the moieties may alternatively eliminate or attenuate any undesirable side effect of the protein complex and the like.
• Moieties capable of mediating such effects are disclosed, for example, in Remington's Pharmaceutical Sciences, 18th ed., Mack Publishing Co., Easton, PA (1990).
• fragment is used to indicate a polypeptide derived from the amino acid sequence of the proteins, of the complexes having a length less than the full-length polypeptide from which it has been derived.
• a fragment may, for example, be produced by proteolytic cleavage of the full-length protein.
• the fragment is obtained recombinantly by appropriately modifying the DNA sequence encoding the proteins to delete one or more amino acids at one or more sites of the C-terminus, N-terminus, and/or within the native sequence.
• Fragments of a protein are useful for screening for substances that act to modulate signal transduction, as described herein. It is understood that such fragments may retain one or more characterizing portions of the native complex. Examples of such retained characteristics include: catalytic activity; substrate specificity; interaction with other molecules in the intact cell; regulatory functions; or binding with an antibody specific for the native complex, or an epitope thereof.
• variant polypeptide which either lacks one or more amino acids or contains additional or substituted amino acids relative to the native polypeptide.
• the variant may be derived from a naturally occurring complex component by appropriately modifying the protein DNA coding sequence to add, remove, and/or to modify codons for one or more amino acids at one or more sites of the C-terminus, N-terminus, and/or within the native sequence. It is understood that such variants having added, substituted and/or additional amino acids retain one or more characterizing portions of the native protein, as described above.
• a functional derivative of a protein with deleted, inserted and/or substituted amino acid residues may be prepared using standard techniques well-known to those of ordinary skill in the art.
• the modified components of the functional derivatives may be produced using site-directed mutagenesis techniques (as exemplified by Adelman et al, 1983, DNA 2:183) wherein nucleotides in the DNA coding the sequence are modified such that a modified coding sequence is modified, and thereafter expressing this recombinant DNA in a prokaryotic or eukaryotic host cell, using techniques such as those described above.
• proteins with amino acid deletions, insertions and/or substitutions may be conveniently prepared by direct chemical synthesis, using methods well-known in the art.
• the functional derivatives of the proteins typically exhibit the same qualitative biological activity as the native proteins.
• Table 1 documents the name of each gene, the classification of each gene, the positions of the open reading frames within the sequence, and the length of the corresponding peptide. From left to right the data presented is as follows: “Gene Name”, “ID#na”, “ID#aa”, “FL/Cat”, “Superfamily”, “Group”, “Family”, “NA ength”, “ORF Start”, “ORF End”, “ORF Length”, and “AA_length”.
• “Gene name” refers to name given the sequence encoding the kinase or kinase-like enzyme.
• Each gene is represented by "SGK” designation followed by a number. The SGK name usually represents multiple overlapping sequences built into a single contiguous sequence (a “contig”).
• ID#na and ID#aa refer to the identification numbers given each nucleic acid and amino acid sequence in this patent.
• FL/Cat refers to the length of the gene, with FL indicating full length, and "Cat' indicating that only the catalytic domain is presented.
• Partial in this column indicates that the sequence encodes a partial protein kinase catalytic domain, [insert* - "FLv” means ????? and "no” means ??????]”Superfamily" identifies whether the gene is a protein kinase or protein-kinase-like.
• Group and “Family” refer to the protein kinase classification defined by sequence homology and based on previously established phylogenetic analysis [Hardie, G. and Hanks S. The Protein Kinase Book, Academic Press (1995) and Hunter T. and Plowman, G. Trends in Biochemical Sciences (1977) 22:18-22 and Plowman G.D. et al. (1999) Proc. Natl. Acad. Sci. 96:13603-13610)].
• NA_length refers to the length in nucleotides of the corresponding nucleic acid sequence.
• ORF start refers to the beginning nucleotide of the open reading frame.
• ORF end refers to the last nucleotide of the open reading frame, excluding the stop codon.
• ORF length refers to the length in nucleotides of the open reading frame (excluding the stop codon).
• AA length refers to the length in amino acids of the peptide encoded in the corresponding nuclei acid sequence.
• Table 2 lists the following features of the genes described in this application: chromosomal localization, single nucleotide polymo ⁇ hisms (SNPs), representation in dbEST, and repeat regions. From left to right the data presented is as follows: “Gene Name”, “ID#na”, “ID#aa”, “FL/Cat”, “Superfamily”, “Group”, “Family”, “Chromosome”, “SNPs”, “dbEST iits", & “Repeats”. The contents of the first 7 columns (i.e.,. "Gene Name”,
• SNPs single nucleotide polymo ⁇ hisms
• dbESThits lists accession numbers of entries in the public database of ESTs (dbEST, http://www.ncbi.nlm.mh.gov/dbEST/index.html) that contain at least 100 bp of 100% identity to the corresponding gene. These ESTs were identified by blastn of dbEST. "Repeats” contains information about the location of short sequences, approximately 20 bp in length, that are of low complexity and that are present in several distinct genes. These repeats were identified by blastn of the DNA sequence against the non-redundant nucleic acid database at NCBI (nrna). To be included in this repeat column, the sequence typically could have 100% identity over its length and typically is present in at least 5 different genes.
• Table 3 lists the extent and the boundaries of the kinase catalytic domains.
• the column headings are: “Gene Name”, “ID#na”, “ID#aa”, “FL/Cat”, “Profile_start”, “Profile_end”, “Kinase_start”, “Kinase_end”, and “profile”.
• the contents of the first 7 columns i.e.,. "Gene Name”, “ID#na”, “ID#aa”, “FL/Cat”, “Superfamily”, “Group”, “Family" are as described above for Table 1.
• “Profile Start”, “Profile End”, “Kinase Start” and “Kinase End” refer to data obtained using a Hidden-Markov Model to define catalytic range boundaries.
• the profile has a length of 261 amino acids, corresponding to the complete protein kinase catalytic domain. Proteins in which the profile recognizes a full length catalytic domain have a “Profile Start” of 1 and a “Profile End” of 261. Genes which have a partial catalytic domain will have a “Profile Start” of greater than 1 (indicating that the beginning of the kinase domain is missing, and/or a “Profile End” of less than 261 (indicating that the C-terminal end of the kinase domain is missing). The boundaries of the catalytic domain within the overall protein are noted in the "Kinase Start” and "Kinase End” columns.
• Profile indicates whether the complete or "Smith Waterman” (partial).
• two hidden Markov models were built. One of them allows for partial matches to the catalytic domain; this is a "local” HMM, similar to Smith- Waterman alignments in sequence matching.
• the other "complete” model allows matches only to the complete catalytic domain; this is a "global” HMM similar toNeedleman-Wunsch alignments in sequence matching.
• the Smith Waterman local model is more specific, allowing for fragmentary matches to the kinase catalytic domain whereas the global "complete” model is more sensitive, allowing for remote homologue identification.
• Table 4 describes the results of Smith Waterman similarity searches (Matrix: PamlOO; gap open/extension penalties 12/2) of the amino acid sequences against the NCBI database of non-redundant protein sequences (http://www.ncbi .nhn.nih. ov/Entrez/protein.html .
• the column headings are: "Gene Name”, “ID#na”, “ID#aa”, “FL/Cat”, “Superfamily”, “Group”, “Family”, “Pscore”, “aa ength”, “aa_ID_match”, “%Identity”, “%Similar”, “ACC#_nraa_match", and “Description".
• the contents of the first 8 columns i.e.,.
• Table 5 gives results of a PCR screen of 96 human cDNA sources for the two kinases exemplified in this application. A plus sign (+) indicates the presence of a band on an agarose gel of the expected size for the target kinase.
• the columns in table 5 are as follows: "Tissue_name”, “RNA_source” ("Clontech”: from Clontech fric (http://www.clontech.com), “Sugen”: (from in-house sources); “NCI”: (derived in-house from from human tumor cell lines), "Tissue” (tissue from which RNA is derived), and PCR screening results (SGK341 and SGK 351), followed by "Comments”.
• HPAEC Sugen renal proximal tubule epithelial cells
• HMEC Sugen coronary artery endothelial cells
• HMEC Sugen coronary artery endothelial cells
• SK-MEL-2 Cell Line MEL Malignant melanoma, metastasis to skin of thigh
• Novel kinases were identified from the Celera human genomic sequence databases, and from the public Human Genome Sequencing project (http://www.ncbi.nlm.nih. gov using a hidden Markov model (HMMR) built with 70 mammalian and yeast kinase catalytic domain sequences. These sequences were chosen from a comprehensive collection of kinases such that no two sequences had more than 50% sequence identity.
• HMMR hidden Markov model
• the genomic database entries were translated in six open reading frames and searched against the model using a Timelogic Decypher box with a Field programmable array (FPGA) accelerated version of HMMR2.1.
• FPGA Field programmable array
• the nucleic acid sequences were then clustered using the Pangea Clustering tool to eliminated repetitive entries.
• the putative protein kinase sequences were then sequentially run through a series of queries and filters to identify novel protein kinase sequences.
• the HMMR identified sequences were searched using BLASTN and BLASTX against a nucleotide and amino acid repository containing 634 known human protein kinases and all subsequent new protein kinase sequences as they are identified.
• the output was parsed into a spreadsheet to facilitate elimination of known genes by manual inspection. Two models were developed, a "complete" model and a "partial” or Smith Waterman model.
• the partial model was used to identify sub-catalytic kinase domains, whereas the complete model was used to identify complete catalytic domains.
• the selected hits were then queried using BLASTN against the public nrna and EST databases to confirm they are indeed unique, hi some cases the novel genes were judged to be homologues of previously identified rodent or vertebrate protein kinases.
• Extension of partial DNA sequences to encompass the full-length open-reading frame was carried out by several methods. Iterative blastn searching of the cDNA databases listed in Table 9 was used to find cDNAs that extended the genomic sequences. "LifeSeqGold" databases are from fricyte Genomics, Inc (http://www.incyte.com/).
• NCBI databases are from the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/ ). All blastn searches were conducted using a penalty for a nucleotide mismatch of -3 and reward for a nucleotide match of 1.
• the gapped blast algorithm is described in: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25 :3389-3402).
• Another method for defining DNA extensions from genomic sequence used iterative searches of genomic databases through the Genscan program to predict exon splicing. These predicted genes were then assessed to see if they represented "real" extensions of the partial genes based on homology to related kinases. Another method involved using the Genewise program
• the sources for the sequence information used to extend the genes in the provisional patents are listed below.
• the accession numbers of the protein ortholog and the genomic DNA are given. (Genewise uses the ortholog to assemble the coding sequence of the target gene from the genomic sequence).
• the amino acid sequences for the orthologs were obtained from the NCBI non-redundant database of proteins .(http://www.ncbi.nlm.nih.gov/Entrez/protein.html).
• the genomic DNA came from two sources: Celera and NCBI-NRNA, as indicated below. cDNA sources are also listed below.
• Genscan predictions were used as input for Genscan predictions to predict splice sites [Burge and Karlin, JMB (1997) 268(l):78-94)].
• HGP Human Genome Project
• NCBI National Center for Biotechnology Information.
• SGK341, SEQ ED NOS: 1 and 3 is 4480 nucleotides long.
• the open reading frame starts at position 1 and ends at position 4080, giving an ORF length of 4080 nucleotides.
• the stop codon is from 4081 to 4083.
• the 3' untranslated region runs from nucleotides 4081 to 4480.
• the predicted protein is 1360 amino acids long.
• This sequence is a full length kinase gene. It is classified as a protein kinase in the STE11 family. This gene maps to chromosomal position Xp22.1. Amplification of genes in this region (Xp) have been associated with increased risk of colorectal cancer (Knuutila, et al.).
• This gene contains three single nucleotide polymorphisms, at nucleotides 4120, 4166, and 4335.
• the 10 nucleotides preceding the polymorphism are given to reduce any ambiguity in the position of the polymo ⁇ hisms). All of the SNPs are in the 3' non-coding region.
• the nucletide sequence for this gene is represented in the public database of expressed sequence tags by the following ESTs: AV710158, AA410835, and BF132430. There are no small repeat regions in this gene.
• SGK351 (SEQ ID NO:2 and 4) is 594 nucleotides long. The open reading frame starts at position 1 and ends at position 594, giving an ORF length of 594 nucleotides. The predicted protein is 198 amino acids long. This sequence contains a partial kinase catalytic domain. It is classified as a Protein Kinase of the AGC group and the S6K family. This gene maps to cytogenetic region 17q23. Amplification of this chromosomal position (17q22-q25 ) has been assosciated with increased incidence of breast carcinoma and bladder cancer (Knuutila, et al.). This gene does not contain mapped candidate single nucleotide polymorphisms. No ESTs representing this gene in were not found in dbEST. This gene has repetitive sequence at nucleotide positions 109 - 131.
• the gene expression patterns for selected genes were studied using a PCR screen of 96 human tissues. This technique does not yield quantitative expression levels between tissues, but does identify which tissues express the gene at a level detectable by PCR and those which do not.
• SGK341, SEQ ID NOS: 1 and 3 encodes a protein that is 1360 amino acids long. It is classified as a protein kinase in the STEl 1 family.
• the kinase domain in this protein matches the hidden Markov profile for a full length kinase domain of 261 amino acids from profile position 3 to profile position 261.
• the position of the kinase catalytic region within the encoded protein is from amino acid 701 to amino acid 955.
• SGK351 SEQ ID NOS: 2 and 4, encodes a protein that is 198 amino acids long. It is classified as (superfamily/group/family): Protein Kinase, AGC, S6K.
• the kinase domain in this protein matches the hidden Markov profile for a full length kinase domain of 261 amino acids from profile position 24 to profile position 261.
• the position of the partial kinase catalytic region within the encoded protein is from amino acid 1 to amino acid 175.
• PCR Screening Screening for expression sources by PCR from ds cDNA templates
• dscDNA templates were prepared by PCR amplification of symmetrically-tagged reverse transcriptase sscDNA products generated as described in detail under Materials and Methods for the Tissue Array Gene Expression protocol.
• the tissue sources amplified are listed, for example, in Table 7.
• the amplification conditions were as follows: per 200 microl of PCR reaction, added 100 microl of Premix TaKaRa ExTaq, 20.0 microl of pwo DNA polymerase (1/10 dilution made as follows: 1 microl pwo (5 units/microl), 1 microl lOx PCR buffer with 20 mM MgSO4, 8 microl water), 4.0 microl sscDNA template (reverse transcriptase product), 8.0 microl 10 pmoles/microl (10 microM) primer (AAGCAGTGGTAACAACGCAGAGT ) (1.0 microM final cone.) and 68.0 microl H 2 0.
• the reaction was amplified according to the following regiment: hot start (95°C for 1 min), 95°C for 1 min, 24 cycles, 95°C for 20 s, 65°C for 30 s, 68°C for 6 min, 68°C for 10 min, 1 cycle and 4°C forever.
• hot start 95°C for 1 min
• 95°C for 1 min 95°C for 1 min
• 24 cycles 95°C for 20 s
• 68°C for 6 min 68°C for 10 min
• 1 cycle and 4°C forever 5-10 microl of product were applied to an agarose gel together with lkb ladder size standards to assess the yield and uniformity of the product.
• a ;positive sign(+) Table 5 indicates the presence of the PCT product at the expected size. Products were cut out for sequence verification.
• the oligonucleotides used to screen the DNA sources, and the size of the PCR product, are listed below.
• SEQID_NA_1 SGK341 (Ste/Stell) 5' primer CAGCAGGCAGTACGGTGGAGC
• SEQ ID NO: 1, SGK341 was successfully identified by PCR from the following human tissues/cell lines uterus, fetal brain and heart. This gene is restricted in its expression.
• SEQ ID NO:2 SGK351 was successfully identified by PCR from the following human tissues/cell lines: fetal liver, thymus, pancreas , pituitary gland , placenta , prostate, salivary gl. , skeletal muscle , small intestine , spinal cord , Spleen , stomach, thyroid gland , trachea , uterus , adrenal gland , fetal brain , fetal kidney , fetal lung , heart , kidney , liver , lung , lymph node ,Heart ,HPAEC, RPTEC, HMEC, HCAEC, 458 medullo RNA, A549/ATCC , MDA-MB-231, Hs 578T, MCF-7/ADR-RES, Malme-3M, A498, COLO 205, CCRF-CEM, SF-539, SF-295, U251, and SNB-19. This gene has a broad expression pattern.
• EXAMPLE 2c Classification of polypeptides exhibiting kinase activity among defined groups STE Group
• SEQ ID NO:l, SGK341 is a novel member of the STE family of kinases.
• the STE family of protein kinases represent key regulators of multiple signal transduction pathways important in cell proliferation, survival, differentiation and response to cellular stress.
• the STE group of protein kinases includes as its major prototypes the NEK kinases as well as the STE7, STEl 1 and STE20 family of sterile protein kinases.
• SGK341 (SEQID_NA_#1) represents a novel STEl 1 family member of the STE group.
• the encoded protein shares 58% identity to ASK1, a kinase involved in regulating cell survival (Hatai, et al. JBiol Chem 2000 Aug 25;275(34):26576-81).
• SGK341 (SEQID_NA#_1) may play a role in cell survival, as well as other important signalling pathways regulated by STE family members.
• SEQ ID NO: 2 is a member of the AGC group of protein kinases.
• the AGC group of protein kinases includes as its major prototypes protein kinase C (PKC), cAMP- dependent protein kinases (PKA), the G protein-coupled receptor kinases [(ARK and rhodopsin kinase (GRK1)] as well as p70S6K and AKT.
• PLC protein kinase C
• PKA cAMP- dependent protein kinases
• GRK1 G protein-coupled receptor kinases
• SEQID_NA_2 SGK351 belongs specifically to the S6K family of AGC group kinases. It is 97% identical over a 198 amino acid region to human ribosomal protein S6 kinase (P23443).
• Ribosomal protein S6 protein kinases consist of at least 8 members (RSK1, RSK2, RSK3, RSK4, MSKl, MSK2, p70S6K and p70S6Kb). Ribosomal protein S6 protein kinases play important pleotropic functions, among them is a key role in the regulation of mRNA translation during protein biosynthesis (Eur J Biochem 2000 Nov; 267(21):6321-30, Exp Cell Res. 1999 Nov 25;253 (l):100-9, Mol Cell Endocrinol 1999 May 25;151(l-2):65-77).
• SEQID_NA_2 SGK351 may represent an additional member of the family of S6 kinases with a potential role in cancer, inflammation, as well as other disease conditions.
• RNAs are isolated using the Guanidine Salts/Phenol extraction protocol of Chomczynski and Sacchi (P. Chomczynski andN. Sacchi, Anal. Biochem. 162, 156 (1987)) from primary human tumors, normal and tumor cell lines, normal human tissues, and sorted human hematopoietic cells. These RNAs are used to generate single-stranded cDNA using the Superscript Preamplification System (GIBCO BRL, Gaithersburg, MD; Gerard, GF et al. (1989), FOCUS 11, 66) under conditions recommended by the manufacturer.
• GEBCO BRL Superscript Preamplification System
• a typical reaction uses 10 ⁇ g total RNA with 1.5 ⁇ g oligo(dT) 12-18 in a reaction volume of 60 ⁇ L.
• the product is treated with RNaseH and diluted to 100 ⁇ L with H 2 0.
• 1-4 ⁇ L of this sscDNA is used in each reaction.
• PCR reactions are performed using degenerate primers applied to multiple single- stranded cDNAs.
• the primers are added at a final concentration of 5 ⁇ M each to a mixture containing 10 mM TrisHCl, pH 8.3, 50 mM KC1, 1.5 mM MgCl 2 , 200 ⁇ M each deoxynucleoside triphosphate, 0.001 % gelatin, 1.5 U AmpliTaq DNA Polymerase (Perkin- Elmer/Cetus), and 1-4 ⁇ L cDNA.
• the cycling conditions are 94 °C for 30 s, 50 °C for 1 min, and 72 °C for 1 min 45 s for 35 cycles.
• PCR fragments migrating between 300-350 bp are isolated from 2% agarose gels using the GeneClean Kit (BiolOl), and T-A cloned into the pCRII vector (Invitrogen Corp. U.S.A.) according to the manufacturer's protocol.
• Colonies are selected for mini plasmid DNA-preparations using Qiagen columns and the plasmid DNA is sequenced using a cycle sequencing dye-terminator kit with AmpliTaq DNA Polymerase, FS (ABI, Foster City, CA). Sequencing reaction products are run on an ABI Prism 377 DNA Sequencer, and analyzed using the BLAST alignment algorithm (Altschul, S.F. et al, J.Mol.Biol. 215: 403-10).
• PCR strategies are employed to connect various PCR fragments or ESTs using exact or near exact oligonucleotide primers. PCR conditions are as described above except the annealing temperatures are calculated for each oligo pair using the formula: Tm : 4(G+C)+2(A+T).
• Northern blot analysis Northern blots are prepared by running 10 ⁇ g total RNA isolated from 60 human tumor cell lines (such as HOP-92, EKVX, NCI-H23, NCI-H226, NCI-H322M, NCI-H460, NCI-H522, A549, HOP-62, OVCAR-3, OVCAR-4, OVCAR-5, OVCAR-8, IGROV1, SK- OV-3, SNB-19, SNB-75, U251, SF-268, SF-295, SF-539, CCRF-CEM, K-562, MOLT-4, HL-60, RPMI 8226, SR, DU-145, PC-3, HT-29, HCC-2998, HCT-116, SW620, Colo 205, HTC15, KM-12, UO-31, SN12C, A498, CaKil, RXF-393, ACHN, 786-0, TK-10, LOX IMVI, Mal
• Filters are hybridized with random primed [ ⁇ 32 P]dCTP-labeled probes synthesized from the inserts of several of the kinase genes. Hybridization is performed at 42 °C overnight in 6X SSC, 0.1% SDS, IX Denhardt's solution, 100 ⁇ g/mL denatured herring sperm DNA with 1-2 x 10 6 cpm mL of 32 P-labeled DNA probes. The filters are washed in 0.1X SSC/0.1% SDS, 65 °C, and exposed on a Molecular Dynamics phosphorimager.
• RNA is isolated from a variety of normal human tissues and cell lines. Single stranded cDNA is synthesized from 10 ⁇ g of each RNA as described above using the Superscript Preamplification System (GibcoBRL). These single strand templates are then used in a 25 cycle PCR reaction with primers specific to each clone. Reaction products are elecfrophoresed on 2% agarose gels, stained with ethidium bromide and photographed on a UV light box. The relative intensity of the STK-specific bands were estimated for each sample.
• Plasmid DNA array blots are prepared by loading 0.5 ⁇ g denatured plasmid for each kinase on a nylon membrane.
• the [ ⁇ 32 P]dCTP labeled single stranded DNA probes are synthesized from the total RNA isolated from several human immune tissue sources or tumor cells (such as thymus, dendrocytes, mast cells, monocytes, B cells (primary, Jurkat, RPMI8226, SR), T cells (CD8/CD4+, THl, TH2, CEM, MOLT4), K562 (megakaryocytes).
• Hybridization is performed at 42 °C for 16 hours in 6X SSC, 0.1% SDS, IX Denhardt's solution, 100 ⁇ g/mL denatured herring sperm DNA with 10 6 cpm/mL of [ ⁇ 32 P]dCTP labeled single sfranded probe.
• the filters are washed in 0.1X SSC/O.P/o SDS, 65 °C, and exposed for quantitative analysis on a Molecular Dynamics phosphorimager.
• Expression constructs are generated for some of the human cDNAs including: a) full- length clones in a pCDNA expression vector; b) a GST-fusion construct containing the catalytic domain of the novel kinase fused to the C-terminal end of a GST expression cassette; and c) a full-length clone containing a Lys to Ala (K to A) mutation at the predicted ATP binding site within the kinase domain, inserted in the pCDNA vector.
• the "K to A" mutants of the kinase might function as dominant negative constructs, and will be used to elucidate the function of these novel STKs.
• Proteins in SDS PAGE are transferred to immobilon membrane.
• the washing buffer is PBST (standard phosphate-buffered saline pH 7.4 + 0.1% Triton X-100).
• Blocking and antibody incubation buffer is PBST +5% milk.
• Antibody dilutions varied from 1 : 1000 to 1:2000.
• the pcDNA expression plasmids (10 ⁇ g DNA 100 mm plate) containing the kinase constructs are introduced into 293 cells with lipofectamine (Gibco BRL). After 72 hours, the cells are harvested in 0.5 mL solubilization buffer (20 mM HEPES, pH 7.35, 150 mM NaCI, 10% glycerol, 1% Triton X-100, 1.5 mM MgCl 2 , 1 mM EGTA, 2 mM phenylmethylsulfonyl fluoride, 1 ⁇ g/mL aprotinin).
• a 10 cm plate of 293 cells is washed with PBS and solubilized on ice with 2 mL PBSTDS containing phosphatase inhibitors (10 mM NaHPO 4 , pH 7.25, 150 mM NaCI, 1% Triton X-100, 0.5% deoxycholate, 0.1% SDS, 0.2% sodium azide, 1 mM NaF, 1 mM EGTA, 4 mM sodium orthovanadate, 1% aprotinin, 5 ⁇ g/mL leupeptin).
• phosphatase inhibitors 10 mM NaHPO 4 , pH 7.25, 150 mM NaCI, 1% Triton X-100, 0.5% deoxycholate, 0.1% SDS, 0.2% sodium azide, 1 mM NaF, 1 mM EGTA, 4 mM sodium orthovanadate, 1% aprotinin, 5 ⁇ g/mL leupeptin).
• HNTG (20 mM HEPES, pH 7.5/150 mM NaCI, 0,1% Triton X-100, 10% glycerol).
• the immunopurified kinases on sepharose beads are resuspended in 20 ⁇ L HNTG plus 30 mM MgCl 2 , 10 mM MnCl 2 , and 20 ⁇ Ci [ ⁇ 32 P]ATP (3000 Ci/mmol).
• the kinase reactions are run for 30 min at room temperature, and stopped by addition of HNTG supplemented with 50 mM EDTA.
• the samples are washed 6 times in HNTG, boiled 5 min in SDS sample buffer and analyzed by 6% SDS-PAGE followed by autoradiography. Phosphoamino acid analysis is performed by standard 2D methods on 32 P-labeled bands excised from the SDS-PAGE gel.
• accession number for the nucleic acid sequence is used to query the Unigene database.
• the site containing the Unigene search engine is: http://www.ncbi.nlm.mh.gov/UniGene/Hs.Home.html.
• a cytogenetic region has been identified by one of these approaches, disease association can be established by searching OMIM with the cytogenetic location.
• OMIM maintains a searchable catalog of cytogenetic map locations organized by disease.
• a thorough search of available literature for the cytogenetic region is also made using Medline (http://www.ncbi.nlm.mh.gov/PubMed/medline.html).
• feferences for association of the mapped sites with chromosomal abnormalities found in human cancer can be found in: Knuutila, et al., Am J Pathol, 1998, 152: 1107-1123.
• the chromosomal regions for mapped genes are listed in Table 2.
• the chromosomal positions were cross-checked with the Online Mendelian Inheritance in Man database (OMIM, http://www.ncbi.nlm.nih.gov/htbin-post/Omim ⁇ which tracks genetic information for many human diseases, including cancer. References for association of the mapped sites with chromosomal abnormalities found in human cancer can be found in: Knuutila, et al., Am J Pathol, 1998, 152:1107- 1123. A third source of information on mapped positions was searching published literature (at NCBI, http ://www.ncbi.nlm.nih. gov/entrez/query.fcgi) for documented association ofthe mapped position with human disease.
• SNPs single nucleotide polymorphisms
• Candidate SNPs for the genes in this patent were identified by blastn searching the nucleic acid sequences against the public database of sequences containing documented SNPs (dbSNP: sequence files were downloaded from ftp://ncbi.nlm.nih.gov/SNP/human/rs-fasta/ and ftp://ncbi.nlm.mh.gov/SNP/human/ss-fasta/ and used to create a blast database).
• SNPs were also identified by comparing several databases of expressed genes (dbEST, NRNA) and genomic sequence (i.e., NRNA) for single basepair mismatches. The results are shown in Table 2, in the column labeled "SNPs". These are candidate SNPs - their actual frequency in the human population was not determined.
• the code below is standard for representing DNA sequence:
• R G or A, puRine
• N A,C,GorT,aNy
• SGK341 maps to chromosomal position Xp22.1. Amplification of genes in this region (Xp) have been associated with increased risk of colorectal cancer
• SGK351 maps to cytogenetic region 17q23. Amplification of this chromosomal position (17q22-q25 ) has been assosciated with increased incidence of breast carcinoma and bladder cancer (Knuutila, et al.). This gene does not contain mapped candidate single nucleotide polymorphisms. No ESTs representing this gene in were not found in dbEST. This gene has repetitive sequence at nucleotide positions 109 - 131.
• Nylon membranes are purchased from Boehringer Mannheim. Denaturing solution contains 0.4 M NaOH and 0.6 M NaCI. Neutralization solution contains 0.5 M Tris-HCL, pH 7.0
• Hybridization solution contains 50% formamide, 6X SSPE, 2.5X
• Denhardt's solution 0.2 mg/mL denatured salmon DNA, 0.1 mg/mL yeast tRNA, and 0.2 % sodium dodecyl sulfate. Restriction enzymes are purchased from Boehringer Mannheim.
• Radiolabeled probes are prepared using the Prime-it II kit by Stratagene.
• the beta actin DNA fragment used for a probe template is purchased from Clontech.
• Genomic DNA is isolated from a variety of tumor cell lines (such as MCF-7, MDA-
• MB-231 Calu-6, A549, HCT-15, HT-29, Colo 205, LS-180, DLD-1, HCT-116, PC3, CAPAN-2, MIA-PaCa-2, PANC-1, AsPc-1, BxPC-3, OVCAR-3, SKOV3, SW 626 and PA- 1, and from two normal cell lines.
• a 10 ⁇ g aliquot of each genomic DNA sample is digested with EcoR I restriction enzyme and a separate 10 ⁇ g sample is digested with Hind III restriction enzyme.
• the restriction-digested DNA samples are loaded onto a 0.7% agarose gel and, following elecfrophoretic separation, the DNA is capillary-transferred to a nylon membrane by standard methods (Sambrook, J. et al (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory).
• Phage display provides a method for isolating molecular interactions based on affinity for a desired bait. cDNA fragments cloned as fusions to phage coat proteins are displayed on the surface of the phage. Phage(s) interacting with a bait are enriched by affinity purification and the insert DNA from individual clones is analyzed.
• Protein domains to be used as baits are generated as C-terminal fusions to GST and expressed in E. coli.
• Peptides are chemically synthesized and biotinylated at the N-terminus using a long chain spacer biotin reagent.
• bound phage is eluted in 100 ⁇ L of 1% SDS and plated on agarose plates to obtain single plaques. Identification of insert DNAs
• EXAMPLE 11 FLK-1 An ELISA assay was conducted to measure the kinase activity of the FLK-1 receptor and more specifically, the inhibition or activation of TK activity on the FLK-1 receptor. Specifically, the following assay was conducted to measure kinase activity of the FLK-1 receptor in cells genetically engineered to express Flk-1. Materials and Reagents
• PBS Gibco Catalog No. 450-1300EB
• TBSW Buffer 50 mM Tris (pH 7.2), 150 mM NaCI and 0.1 % Tween-20
• Ethanolamine stock (10% ethanolamine (pH 7.0), stored at 4 °C);
• HNTG buffer (20 mM HEPES buffer (pH 7.5), 150 mM NaCI, 0.2% Triton X- 100, and 10% glycerol);
• FBS Gibco (catalog no. 16000-028);
• VEGF vascular endothelial growth factor
• PeproTech, Inc. catalog no. 100-20
• Affinity purified anti-FLK-1 antiserum
• ABTS 2,2-azino-bis(3-ethylbenz-thiazoline-6-sulfonic acid
• media should be removed from the cells and washed one time with 200 ⁇ l/well PBS.
• HNTG formulation includes sodium ortho vanadate, sodium pyrophosphate and EDTA.
• Assay 1 EGF Receptor-HER2 Chimeric Receptor Assay hi Whole Cells. HER2 kinase activity in whole EGFR-NIH3T3 cells was measured as described below:
• EGF stock concentration: 16.5 ILM; EGF 201, TOYOBO, Co., Ltd. Japan.
• UBI 05-101
• Anti-phosphotyrosine antibody (anti-Ptyr) (polyclonal) (see, Fendley, et al, supra).
• Detection antibody Goat anti-rabbit IgG horse radish peroxidase conjugate, TAGO, Inc., Burlingame, CA.
• Coat ELISA plates (Corning, 96 well, Cat. #25805-96) with 05-101 antibody at 0.5 g per well in PBS, 100 ⁇ l final volume/well, and store overnight at 4 °C. Coated plates are good for up to 10 days when stored at 4 °C.
• N1H3T3 cell line overexpressing a chimeric receptor containing the EGFR extracellular domain and intracellular HER2 kinase domain can be used for this assay.
• EGF ligand dilute stock EGF in DMEM so that upon transfer of 10 ⁇ l dilute EGF (1:12 dilution), 100 nM final concentration is attained.
• HNTG* ( ml): HNTG stock 2.0 ml milli-Q H 2 O 7.3 ml
• the maximal phosphotyrosine signal is determined by subtracting the value of the negative controls from the positive controls. The percent inhibition of phosphotyrosine content for extract-containing wells is then calculated, after subtraction of the negative controls.
• EXAMPLE 13 PDGF-R ELISA All cell culture media, glutamine, and fetal bovine serum were purchased from Gibco Life Technologies (Grand Island, NY) unless otherwise specified. All cells were grown in a humid atmosphere of 90-95% air and 5-10% CO 2 at 37 °C. All cell lines were routinely subcultured twice a week and were negative for mycoplasma as determined by the Mycotect method (Gibco).
• cells (U124 2, obtained from Joseph Schlessinger, NYU) were grown to 80-90%) confluency in growth medium (MEM with 10% FBS, NEAA, 1 mM NaPyr and 2 mM GLN) and seeded in 96-well tissue culture plates in 0.5%> serum at 25,000 to 30,000 cells per well. After overnight incubation in 0.5% serum-containing medium, cells were changed to serum-free medium and treated with test compound for 2 hr in a 5% CO , 37 °C incubator.
• Cells were then stimulated with ligand for 5-10 minute followed by lysis with HNTG (20 mM Hepes, 150 mM NaCI, 10% glycerol, 5 mM EDTA, 5 mM Na 3 VO 4 , 0.2% Triton X-100, and 2 mM NaPyr).
• HNTG 20 mM Hepes, 150 mM NaCI, 10% glycerol, 5 mM EDTA, 5 mM Na 3 VO 4 , 0.2% Triton X-100, and 2 mM NaPyr.
• Cell lysates (0.5 mg/well in PBS) were transferred to ELISA plates previously coated with receptor-specific antibody and which had been blocked with 5% milk in TBST (50 mM Tris-HCl pH 7.2, 150 mM NaCI and 0.1% Triton X-100) at room temperature for 30 min. Lysates were incubated with shaking for 1 hour at room temperature.
• the plates were washed with TBST four times and then incubated with polyclonal anti-phosphotyrosine antibody at room temperature for 30 minutes. Excess anti- phosphotyrosine antibody was removed by rinsing the plate with TBST four times. Goat anti-rabbit IgG antibody was added to the ELISA plate for 30 min at room temperature followed by rinsing with TBST four more times.
• ABTS 100 mM citric acid, 250 mM Na 2 HPO 4 and 0.5 mg/ml 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) plus H 2 O 2 (1.2 ml 30% H 2 O 2 to 10 ml ABTS) was added to the ELISA plates to start color development. Absorbance at 4 10 nm with a reference wavelength of 630 nm was recorded about 15 to 30 min after ABTS addition.
• the following protocol may be used to measure phosphotyrosine level on IGF-I receptor, which indicates IGF-I receptor tyrosine kinase activity.
• the following materials and reagents were used: 1.
• the cell line used in this assay is 3T3/IGF-1R, a cell line genetically engineered to overexpresses IGF-1 receptor.
• NIH3T3/IGF-1R is grown in an incubator with 5% CO 2 at 37 °C.
• the growth media is DMEM + 10% FBS (heat inactivated)+ 2 mM L-glutamine.
• Blocking Buffer TBST plus 5% Milk (Carnation Instant Non-Fat Dry Milk).
• TBS (10X) Stock solution of TBS (10X) is prepared, and Triton X-100 is added to the buffer during dilution.
• Triton X-100 0.2% Stock solution (5X) is prepared and kept at 4 °C.
• EDTA/HC1 0.5 M pH 7.0 (NaOH) as 100X stock.
• Na 3 VO 4 0.5 M as 100X stock and aliquots are kept in -80 °C.
• Insulin-like growth factor- 1 from Promega (Cat# G5111 ) .
• ABTS (2,2'-azinobis(3-ethylbenzthiazolinesulfonic acid)) solution: Citric acid 100 mM Na 2 HPO 4 250 mM (pH 4.0/1 N HCI) ABTS 0.5 mg/ml
• ABTS solution should be kept in dark and 4 °C. The solution should be discarded when it turns green. 15. Hydrogen Peroxide: 30%) solution is kept in the dark and at 4 °C.
• All the following steps are conducted at room temperature unless it is specifically indicated. All ELISA plate washings are performed by rinsing the plate with tap water three times, followed by one TBST rinse. Pat plate dry with paper towels.
• the cells grown in tissue culture dish (Corning 25020- 100) to 80-90%> confluence, are harvested with Trypsin-EDTA (0.25%, 0.5 ml/D-100, GIBCO).
• EXAMPLE 15 EGF Receptor ELISA
• EGF Receptor kinase activity in cells genetically engineered to express human EGF-R was measured as described below:
• UBI 05-101 (UBI) (a monoclonal antibody recognizing an EGFR extracellular domain).
• Anti-phosphotyosine antibody (anti-Ptyr) (polyclonal).
• Detection antibody Goat anti-rabbit IgG horse radish peroxidase conjugate, TAGO, Inc., Burlingame, CA.
• Coat ELISA plates (Corning, 96 well, Cat. #25805-96) with 05-101 antibody at 0.5 ⁇ g per well in PBS, 150 ⁇ l final volume/well, and store overnight at 4 °C. Coated plates are good for up to 10 days when stored at 4 °C.
• NIH 3T3/C7 cell line (Honegger, et al, 1987, Cell 51:199-209) can be use for this assay.
• EGF ligand dilute stock EGF in DMEM so that upon transfer of 10 ⁇ l dilute EGF (1:12 dilution), 25 nM final concentration is attained.
• HNTG* comprises: HNTG stock (2.0 ml), milli-Q H 2 O (7.3 ml), EDTA, 100 mM, pH 7.0 (0.5 ml), Na 3 VO 4 0.5 M (0.1 ml) and Na 4 (P 2 O 7 ), 0.2 M (0.1 ml).
• HNTG* to cells, 100 ⁇ l per well. Place on ice for 5 minutes. Meanwhile, remove blocking buffer from other ELISA plate and wash with TBST as described above.
• the maximal phosphotyrosine signal is determined by subtracting the value of the negative controls from the positive controls. The percent inhibition of phosphotyrosine content for extract-containing wells is then calculated, after subtraction of the negative controls.
• This assay determines Met tyrosine kinase activity by analyzing Met protein tyrosine kinase levels on the Met receptor.
• HNTG (5X stock solution): Dissolve 23.83 g HEPES and 43.83 g NaCI in about 350 ml dH 2 O. Adjust pH to 7.2 with HCI or NaOH, add 500 ml glycerol and 10 ml Triton X-100, mix, add dH 2 O to 1 L total volume. To make 1 L of IX working solution add 200 ml 5X stock solution to 800 ml dH O, check and adjust pH as necessary, store at 4 °C.
• PBS Dulbecco's Phosphate-Buffered Saline
• Gibco Cat. # 450-1300EB IX solution
• Blocking Buffer in 500 ml dH 2 O place 100 g BSA, 12.1 g Tris-pH7.5, 58.44 g NaCI and 10 ml Tween-20, dilute to 1 L total volume. 4.
• Kinase Buffer To 500 ml dH 2 O add 12.1 g TRIS pH7.2, 58.4 g NaCI, 40.7 g MgCl 2 and 1.9 g EGTA; bring to 1 L total volume with dH 2 O.
• Na 3 VO 4 , Fischer Cat. # S454-50, to 1.8 g material add 80 ml MilliQ H 2 O, adjust pH to 10.0 with HCI or NaOH, boil in microwave, cool, check pH, repeat procedure until pH stable at 10.0, add MilliQ H 2 O to 100 ml total volume, make 1 ml aliquots and store at -80°C. 14.
• MgCl 2 , Fischer Cat. # M33-500 make up 1 M solution.
• HEPES Fischer Cat. # BP310-500
• 200 ml MilliQ H 2 O add 59.6 g material, adjust pH to 7.5, bring volume to 250 ml total, sterile filter.
• EMR Transiently Transfected EGFR/Met chimeric cells
• This procedure can be performed the night before or immediately prior to the start of receptor capture.
• Dilute compounds/extracts 1 10 in IX Kinase Buffer in a polypropylene 96 well plate.
• This assay is used to determine src protein kinase activity measuring phosphorylation of a biotinylated peptide as the readout.
• EEEYEEYEEEYEEEYEEEY is prepared by standard procedures well known to those skilled in the art.
• 96 Well ELISA Plate Corning 96 Well Easy Wash, Modified flat Bottom Plate, Corning Cat. #25805-96.
• Vecastain ELITE ABC reagent Vector, Burlingame, CA.
• Anti-src (327) mab Schizosaccharomyces Pombe was used to express recombinant src (Superti-Furga, et al, EMBO J. 12:2625-2634; Superti-Furga, et al, Nature Biochem. 14:600-605).
• S. Pombe strain SP200 h-s leul.32 ura4 ade210
• transformations were pRSP expression plasmids were done by the lithium acetate method (Superti-Furga, supra). Cells were grown in the presence of 1 ⁇ M thiamin to repress expression from the nmtl promoter or in the absence of thiamin to induce expression.
• PBS Dulbecco's Phosphate-Buffered Saline
• GIBCO PBS GIBCO Cat. # 450-1300EB.
• Blocking Buffer 5% Non-fat milk (Carnation) in PBS.
• Carbonate Buffer Na 2 CO 4 from Fischer, Cat. # S495, make up 100 mM stock solution.
• Lysis Buffer 5.0 HEPES (from 1 M stock solution.); 2.74 ml NaCI (from 5 M stock solution); 10 ml glycerol; 1.0 ml TX-100; 0.4 ml EDTA (from a 100 mM stock solution); 1.0 ml PMSF (from a 100 mM stock solution); 0.1 ml Na 3 VO 4 (from a 0.1 M stock solution); bring to 100 ml total volume with MilliQ H 2 O.
• ATP Sigma Cat. # A-7699, make up 10 mM stock solution (5.51 mg/ml).
• TRIS-HC1 Fischer Cat. # BP 152-5, to 600 ml MilliQ H 2 O add 121.14 g material, adjust pH to 7.5 with HCI, bring to 1 L total volume with MilliQ H 2 O.
• Na 3 VO 4 Fischer Cat. # S454-50; to 80 ml MilliQ H 2 O, add 1.8 g material; adjust pH to 10.0 with HCI or NaOH; boil in a microwave; cool; check pH, repeat pH adjustment until pH remains stable after heating/cooling cycle; bring to 100 ml total volume with MilliQ H 2 O; make 1 ml aliquots and store at -80°C.
• MgCl 2 Fischer Cat. # M33-500, make up 1 M stock solution with MilliQ H 2 O.
• HEPES Fischer Cat. # BP 310-500; to 200 ml MilliQ H 2 O, add 59.6 g material, adjust pH to 7.5, bring to 250 ml total volume with MilliQ H 2 O, sterile filter (1 M stock solution).
• TBST Buffer To 900 ml dH 2 O add 6.057 g TRIS and 8.766 g NaCI; adjust pH to 7.2 with HCI, add 1.0 ml Triton-X-100; bring to 1 L total volume with dH 2 O.
• MnCl 2 Fischer Cat. # M87- 100, make up 1 M stock solution with MilliQ H 2 O.
• TBS TriS Buffered Saline
• Kinase Reaction Mixture Amount per assay plate (100 wells): 1.0 ml Kinase Buffer, 200 ⁇ g GST- ⁇ , bring to final volume of 8.0 ml with MilliQ H 2 O.
• Biotin labeled EEEYEEYEEEYEEEYEEEYEEEY Make peptide stock solution (1 mM, 2.98 mg/ml) in water fresh just before use.
• Vectastain ELITE ABC reagent To prepare 14 ml of working reagent, add 1 drop of reagent A to 15 ml TBST and invert tube several times to mix. Then add 1 drop of reagent B. Put tube on orbital shaker at room temperature and mix for 30 minutes.
• This assay is used to determine lck protein kinase activities measuring phosphorylation of GST- ⁇ as the readout.
• Cell lysates Yeast cells expressing lck are pelleted, washed once in water, re- pelleted and stored frozen at -80°C until use.
• GST- ⁇ DNA encoding for GST- ⁇ fusion protein for expression in bacteria obtained from Arthur Weiss of the Howard Hughes Medical Institute at the University of California, San Francisco. Transformed bacteria were grown overnight while shaking at 25°C. GST- ⁇ was purified by glutathione affinity chromatography, Pharmacia, Alameda, CA.
• 96-Well ELISA plate Corning 96 Well Easy Wash, Modified Flat Bottom Plate, Corning Cat. #25805-96.
• Sheep ant-mouse IgG H+L: Jackson Labs Cat. # 5215-005-003.
• Anti-/c/c (3A5) mab Santa Cruz Biotechnology Cat # sc-433.
• Buffer solutions 1. PBS (Dulbecco's Phosphate-Buffered Saline) IX solution: GIBCO PBS, GIBCO Cat. # 450-1300EB.
• Blocking Buffer 100 g BSA, 12.1 g. TRIS-pH7.5, 58.44 g NaCI, 10 ml Tween-20, bring up to 1 L total volume with MilliQ H 2 O. 3.
• Carbonate Buffer Na 2 CO 4 from Fischer, Cat. # S495; make up 100 mM solution with MilliQ H 2 O.
• Kinase Buffer 1.0 ml (from 1 M stock solution) MgCl 2 ; 0.2 ml (from a 1 M stock solution) MnCl 2 ; 0.2 ml (from a 1 M stock solution) DTT; 5.0 ml (from a 1 M stock solution) HEPES; 0.1 ml TX-100; bring to 10 ml total volume with MilliQ H 2 O. 5.
• Lysis Buffer 5.0 HEPES (from 1 M stock solution.); 2.74 ml NaCI (from 5 M stock solution); 10 ml glycerol; 1.0 ml TX-100; 0.4 ml EDTA (from a 100 mM stock solution); 1.0 ml PMSF (from a 100 mM stock solution); 0.1 ml Na 3 VO 4 (from a 0.1 M stock solution); bring to 100 ml total volume with MilliQ H O.
• ATP Sigma Cat. # A-7699, make up 10 mM stock solution (5.51 mg/ml).
• TRIS-HC1 Fischer Cat. # BP 152-5, to 600 ml MilliQ H 2 O add 121.14 g material, adjust pH to 7.5 with HCI, bring to 1 L total volume with MilliQ H 2 O.
• Na 3 VO 4 Fischer Cat. # S454-50; to 80 ml MilliQ H 2 O, add 1.8 g material; adjust pH to 10.0 with HCI or NaOH; boil in a microwave; cool; check pH, repeat pH adjustment until pH remains stable after heating/cooling cycle; bring to 100 ml total volume with MilliQ H 2 O; make 1 ml aliquots and store at -80°C.
• MgCl 2 Fischer Cat. # M33-500, make up 1 M stock solution with MilliQ H 2 O.
• HEPES Fischer Cat. # BP 310-500; to 200 ml MilliQ H 2 O, add 59.6 g material, adjust pH to 7.5, bring to 250 ml total volume with MilliQ H 2 O, sterile filter (IM stock solution).
• TBS TriS Buffered Saline
• Kinase Reaction Mixture Amount per assay plate (100 wells): 1.0 ml Kinase Buffer, 200 ⁇ g GST- ⁇ , bring to final volume of 8.0 ml with MilliQ H 2 O.
• B Preparation of phosphotyrosine antibody-coated ELISA plate.
• UB40 plate 1.0 ⁇ g/well UB40 in 100 ⁇ l of PBS overnight at 4 °C and block with 150 ⁇ l of Blocking Buffer for at least 1 hour.
• C Kinase assay procedure.
• HNTG 5X stock concentration: 100 mM HEPES pH 7.2, 750 mM NaCI,
• PBS Dulbecco's Phosphate-Buffered Saline

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