US20060019252A1 - Genes and polypeptides relating to hepatocellular or colorectal carcinoma - Google Patents

Genes and polypeptides relating to hepatocellular or colorectal carcinoma Download PDF

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US20060019252A1
US20060019252A1 US10/517,151 US51715105A US2006019252A1 US 20060019252 A1 US20060019252 A1 US 20060019252A1 US 51715105 A US51715105 A US 51715105A US 2006019252 A1 US2006019252 A1 US 2006019252A1
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polypeptide
seq
amino acid
acid sequence
polynucleotide
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Yusuke Nakamura
Yoichi Furukawa
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Oncotherapy Science Inc
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University of Tokyo NUC
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Priority to US11/948,790 priority patent/US20080207549A1/en
Priority to US12/699,711 priority patent/US8124341B2/en
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2/00—Peptides of undefined number of amino acids; Derivatives thereof
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/30—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells
    • C07K16/303—Liver or Pancreas
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4748—Tumour specific antigens; Tumour rejection antigen precursors [TRAP], e.g. MAGE
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/30—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells
    • C07K16/3046—Stomach, Intestines
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • G01N33/57419—Specifically defined cancers of colon
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • G01N33/57438—Specifically defined cancers of liver, pancreas or kidney
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6893—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids related to diseases not provided for elsewhere
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value

Definitions

  • the present invention relates to the field of biological science, more specifically to the field of cancer research.
  • the present invention relates to novel genes, WDRPUH, KRZFPUH, PPIL1, and APCDD1, involved in the proliferation mechanism of cells, as well as polypeptides encoded by the genes.
  • the genes and polypeptides of the present invention can be used, for example in the diagnosis of cell proliferative disease, and as target molecules for developing drugs against the disease.
  • Hepatocellular carcinoma (HCC) and colorectal carcinomas are leading causes of cancer death worldwide (Akriviadis et al., Br J Surg 85(10): 1319-31 (1998)).
  • HCC Hepatocellular carcinoma
  • Br J Surg 85(10): 1319-31 (1998) Although recent medical advances have made great progress in diagnosis and therapeutic strategies, a large number of patients with cancers are still diagnosed at advanced stages and their complete cures from the disease are matters of pressing concern. Recent advances in molecular studies have revealed that alteration of tumor suppressor genes and/or oncogenes are involved in carcinogenesis, however the precise mechanisms still remain to be elucidated.
  • Adenomatous polyposis coli APC
  • Axin Axin
  • conductin GSK-3 ⁇
  • GSK-3 ⁇ glycogen synthase kinase-3 ⁇
  • stathmin is also known to be associated with a wide range of cancers (Hanash et al., J Biol Chem 263: 12813-5 (1988); Roos et al., Leukemia 7: 1538-46 (1993); Nylander et al.; Histochem J 27: 155-60 (1995); Friedrich et al., Prostate 27: 102-9 (1995); Bieche et al., Br J Cancer 78: 701-9 (1998)).
  • Stathmin (Sobel et al., J Biol Chem 264: 3765-72 (1989); Sobel et al., Trends Biol Sci 16: 301-5 (1991)) is a cytosolic phosphorprotein consisting of 148 amino acid residues (19 kD) that has also been referred to as p19, prosolin, Lap18, oncoprotein 18, metablastin, and Op 18.
  • the expression of stathmin was revealed, to be very high in various multipotential embryonic carcinoma cells and in multipotential cells of the inner cell mass of the mouse blastocyst (Doye et al., Differentiation 50:89-96 (1992)).
  • Stathmin exists in cells under several non-phosphorylated and phosphorylated forms, the pattern of which is depending on the state of proliferation, differentiation, or activation of the cells in many biological systems (Sobel et al., Trends Biol Sci 16: 301-5 (1991)). Further, the microtuble depolymerizing activity of stathmin is known to be regulated by the changes in its phosphorylation level, and the microtuble depolymerizing activity of stathmin is reported to play a critical role in the regulation of the dynamic instability of microtubles during the different phases of the cell cycle (Marklund et al., EMBO J 15: 5290-8 (1996); Horwitz et al., J Biol Chem 272: 8129-31 (1997)).
  • stathmin Extensive phosphorylation of stathmin occurs during mitosis (Strahler et al., Biochem Biophy Res Commun 185: 197-203 (1992); Luo et al., J Biol Chem 269: 10312-8 (1994); Brattsand et al., Eur J Biochem 220:359-68 (1994)) and seems essential for the progression of the cell cycle.
  • the precise mechanism of the phosphorylation of stathmin and its relation to canceration remains to be elucidated.
  • cDNA microarray technologies have enabled to obtain comprehensive profiles of gene expression in normal and malignant cells (Okabe et al., Cancer Res 61: 2129-37(2001); Lin et al., Oncogene 21: 4120-8 (2002); Hasegawa et al., Cancer Res 62: 7012-7 (2002)).
  • This approach enables to disclose the complex nature of cancer cells, and helps to understand the mechanism of carcinogenesis. Identification of genes that are deregulated in tumors can lead to more precise and accurate diagnosis of individual cancers, and to develop novel therapeutic targets (Bienz and Clevers, Cell 103:311-20 (2000)).
  • FTIs farnexyltransferase
  • An object of the present invention is to provide novel proteins involved in the proliferation mechanism of hepatocellular or colorectal carcinoma cells and the genes encoding the proteins, as well as methods for producing and using the same in the diagnosis and treatment of hepatocellular carcinoma (HCC) or colorectal cancer.
  • HCC hepatocellular carcinoma
  • the present inventors analyzed the expression profiles of genes in hepatocellular and colorectal carcinogenesis using a genome-wide cDNA microarray containing 23040 genes. From the pharmacological point of view, suppressing oncogenic signals is easier in practice than activating tumor-suppressive effects. Thus, the present inventors searched for genes that are up-regulated during hepatocellular and colorectal carcinogenesis.
  • WDRPUH WD40 repeat protein up-regulated in HCC
  • KRZFPUH Kruppel-type zinc finger protein up-regulated in HCC
  • WDRPUH or KRZFPUH Gene transfer of WDRPUH or KRZFPUH promoted proliferation of cells.
  • reduction of WDRPUH or KRZFPUH expression by transfection of their specific anti-sense S-oligonucleotides inhibited the growth of HCC cells.
  • Many anticancer drugs such as inhibitors of DNA and/or RNA synthesis, metabolic suppressors, and DNA intercalators, are not only toxic to cancer cells but also for normally growing cells.
  • agents suppressing the expression of WDRPUH and KRZFPUH may not adversely affect other organs due to the fact that normal expression of these genes are restricted to testis, and placenta and testis, respectively, and thus may be of great importance for treating cancer.
  • PPIL1 Peptidyl prolyl isomerase-like 1 assigned at chromosomal band 6p21.1 was identified.
  • immunoprecipitation assay revealed that PPIL1 protein associates with SNW1 (SKI interacting protein), a protein involved in transcriptional activity of vitamin D receptor, and stathmin, a cytosolic phosphorprotein involved in progression of the cell cycle.
  • the present inventors also searched for genes regulating ⁇ -catenin/Tcf4 complex that is abnormally up-regulated in hepatomas and colorectal cancers, and identified a novel gene APCDD1 (Down-regulated by adenomatosis polyposis coli) assigned at chromosomal band 18p11.2. Its expression was reduced by the transduction of wild-type APC and elevated in a great majority of colon cancer tissues. Gene transfer of PPIL1 or APCDD1 promoted proliferation of cells that lacked endogenous expression of either of these genes. Furthermore, reduction of PPIL1 or APCDD1 expression by transfection of specific antisense S-oligonucleotides to PPIL1 or APCDD1 inhibited the growth of colorectal cancer cells.
  • APCDD1 Down-regulated by adenomatosis polyposis coli
  • the present invention provides isolated novel genes, WDRPUH, KRZFPUH, PPIL1, and APCDD1, which are candidates as diagnostic markers for cancer as well as promising potential targets for developing new strategies for diagnosis and effective anti-cancer agents. Further, the present invention provides polypeptides encoded by these genes, as well as the production and the use of the same. More specifically, the present invention provides the following:
  • the present application provides novel human polypeptides, WDRPUH, KRZFPUH, PPIL1, and APCDD1, or a functional equivalent thereof, that promotes cell proliferation and is up-regulated in cell proliferative diseases, such as HCC and colorectal carcinoma.
  • the WDRPUH polypeptide includes a putative 620 amino acid protein with 11 WD40 repeat domains encoded by the open reading frame of SEQ ID NO: 1.
  • the WDRPUH polypeptide preferably includes the amino acid sequence set forth in SEQ ID NO: 2.
  • the present application also provides an isolated protein encoded from at least a portion of the WDRPUH polynucleotide sequence, or polynucleotide sequences at least 15%, and more preferably at least 25% complementary to the sequence set forth in SEQ ID NO: 1.
  • the KRZFPUH polypeptide includes a putative 500 amino acid protein with homology to a rat gene zinc finger protein HIT-39 (GenBank Accession No. AF277902) and included a Krupple-type zinc finger domain (KRAB) encoded by the open reading frame of SEQ ID NO: 3.
  • the KRZFPUH polypeptide preferably includes the amino acid sequence set forth in SEQ ID NO: 4.
  • the present application also provides an isolated protein encoded from at least a portion of the KRZFPUH polynucleotide sequence, or polynucleotide sequences at least 15%, and more preferably at least 25% complementary to the sequence set forth in SEQ ID NO: 3.
  • the PPIL1 polypeptide includes a putative 166 amino acid protein showing 98.1% identity to PPIL1, 41.6% to PPIA, 57.4% to Cyp2, and 50% to CypE encoded by the open reading frame of SEQ ID NO: 5.
  • the PPIL1 polypeptide preferably includes the amino acid sequence set forth in SEQ ID NO: 6.
  • the present application also provides an isolated protein encoded from at least a portion of the PPIL1 polynucleotide sequence, or polynucleotide sequences at least 15%, and more preferably at least 25% complementary to the sequence set forth in SEQ ID NO: 5.
  • the APCDD1 polypeptide includes a putative 514 amino acid protein showing 31% identity to endo-1,4-beta-xylanase of Themobacillus xylanilyticus encoded by the open reading frame of SEQ ID NO: 7.
  • the APCDD1 polypeptide preferably includes the amino acid sequence set forth in SEQ ID NO: 8.
  • the present application also provides an isolated protein encoded from at least a portion of the APCDD1 polynucleotide sequence, or polynucleotide sequences at least 15%, and more preferably at least 25% complementary to the sequence set forth in SEQ ID NO: 7.
  • the present invention further provides novel human genes, WDRPUH and KRZFPUH, whose expressions are markedly elevated in a great majority of HCCs as compared to corresponding non-cancerous liver tissues.
  • the isolated WDRPUH gene includes a polynucleotide sequence as described in SEQ ID NO: 1.
  • the WDRPUH cDNA includes 2152 nucleotides that contain an open reading frame of 1860 nucleotides.
  • the present invention further encompasses polynucleotides which hybridize to and which are at least 15%, and more preferably at least 25% complementary to the polynucleotide sequence set forth in SEQ ID NO: 1, to the extent that they encode a WDRPUH protein or a functional equivalent thereof.
  • the isolated KRZFPUH gene includes a polynucleotide sequence as described in SEQ ID NO: 3.
  • the KRZFPUH cDNA includes 2744 nucleotides that contain an open reading frame of 1500 nucleotides.
  • the present invention further encompasses polynucleotides which hybridize to and which are at least 15%, and more preferably at least 25% complementary to the polynucleotide sequence set forth in SEQ ID NO: 3, to the extent that they encode a KRZFPUH protein or a functional equivalent thereof. Examples of such polynucleotides are degenerates and allelic mutants of SEQ ID NO: 3.
  • the present invention provides a novel human gene, PPIL1, whose expression is markedly elevated in a great majority of colorectal cancers as compared to corresponding non-cancerous tissues.
  • the isolated PPIL1 gene includes a polynucleotide sequence as described in SEQ ID NO: 5.
  • the PPIL1 cDNA includes 1734 nucleotides that contain an open reading frame of 498 nucleotides.
  • the present invention further encompasses polynucleotides which hybridize to and which are at least 15%, and more preferably at least 25% complementary to the polynucleotide sequence set forth in SEQ ID NO: 5, to the extent that they encode a PPIL1 protein or a functional equivalent thereof. Examples of such polynucleotides are degenerates and allelic mutants of SEQ ID NO: 5.
  • the present invention provides a novel human gene, APCDD1, whose expression is markedly elevated in a great majority of primary colon cancers as compared to corresponding non-cancerous tissues and down regulated in response to the transduction of wild-type APC1 into, colon cancer cells.
  • the isolated APCDD1 gene includes a polynucleotide sequence as described in SEQ ID NO: 7.
  • the APCDD1: cDNA includes 2607 nucleotides that, contain an open reading frame of 1542 nucleotides.
  • the present invention further encompasses polynucleotides which hybridize to and which are at least 15%, and more preferably at least 25% complementary to the polynucleotide sequence set forth in SEQ ID NO: 7, to the extent that they encode a APCDD1 protein or a functional equivalent thereof.
  • polynucleotides are degenerates and allelic mutants of SEQ ID NO: 7.
  • an isolated gene is a polynucleotide the structure of which is not identical to that of any naturally occurring polynucleotide or to that of any fragment of a naturally occurring genomic polynucleotide spanning more than three separate genes.
  • the term therefore includes, for example, (a) a DNA which has the sequence of part of a naturally occurring genomic DNA molecule in the genome of the organism in which it naturally occurs; (b) a polynucleotide incorporated into a vector or into the genomic DNA of a prokaryote or eukaryote in a manner such that the resulting molecule is not identical to any naturally occurring vector or genomic DNA; (c) a separate molecule such as a cDNA, a genomic fragment, a fragment produced by polymerase chain reaction (PCR), or a restriction fragment; and (d) a recombinant nucleotide sequence that is part of a hybrid gene, i.e., a gene encoding a fusion polypeptide.
  • the invention provides an isolated polynucleotide that encodes a polypeptide described herein or a fragment thereof.
  • the isolated polypeptide includes a nucleotide sequence that is at least 60% identical to the nucleotide sequence shown in SEQ ID NO: 1, 3, 5, or 7. More preferably, the isolated nucleic acid molecule is at least 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 196%, 97%, 98%, 99%, or more, identical to the nucleotide sequence shown in SEQ ID NO: 1, 3, 5, or 7.
  • an isolated polynucleotide which is longer than or equivalent in length to the reference sequence e.g., SEQ ID NO: 1, 3, 5, or 7
  • the comparison is made with the full length of the reference sequence.
  • the isolated polynucleotide is shorter than the reference sequence, e.g., shorter than SEQ ID NO: 1, 3, 5, or 7, the comparison is made to segment of the reference sequence of the same length (excluding any loop required by the homology calculation).
  • the present invention also provides a method of producing a protein by transfecting or transforming a host cell with a polynucleotide sequence encoding the WDRPUH KRZFPUH, PPIL1, or APCDD1 protein, and expressing the polynucleotide sequence.
  • the present invention provides vectors comprising a nucleotide sequence encoding the WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein, and host cells harboring a polynucleotide encoding the WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein.
  • Such vectors and host cells may be used for producing the WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein.
  • an antibody that recognizes the WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein is also provided by the present application.
  • an antisense polynucleotide e.g., antisense DNA
  • ribozyme e.g., ribozyme
  • siRNA small interfering RNA
  • the present invention further provides a method for diagnosis of cell proliferative diseases that includes determining an expression level of the gene in biological sample of specimen, comparing the expression level of WDRPUH, KRZFPUH, PPIL1, or APCDD1 gene with that in normal sample, and defining a high expression level of the WDRPUH, KRZFPUH, PPIL1, or APCDD1 gene in the sample as having a cell proliferative disease such as cancer.
  • the disease diagnosed by the expression level of WDRPUH or KRZFPUH is suitably a hepatocellular carcinoma; and that detected by the expression level of PPIL1 or APCDD1 is colorectal carcinoma.
  • a method of screening for a compound for treating a cell proliferative disease includes contacting the WDRPUH, KRZFPUH, PPIL1, or APCDD1 polypeptide with test compounds, and selecting test compounds that bind to the WDRPUH, KRZFPUH, PPIL1, or APCDD1 polypeptide.
  • the present invention further provides a method of screening for a compound for treating a cell proliferative disease, wherein the method includes contacting the WDRPUH, KRZFPUH, PPIL1, or APCDD1 polypeptide with a test compound, and selecting the test compound that suppresses the expression level or biological activity of the WDRPUH, KRZFPUH, PPIL1, or APCDD1 polypeptide.
  • Also provided is a method of screening for a compound for treating a cell proliferative disease wherein the method includes contacting a test compound, catenin/Tcf 4 complex, and a reporter gene with a transcriptional regulatory region of APCDD1 comprising the two Tcf/LEF binding motifs under a suitable condition for the expression of the reporter gene, and selecting the test compound that inhibits the expression of the reporter gene.
  • the present invention provides a method of screening for a compound for treating a cell proliferative disease, wherein the method includes contacting PPIL1 and stathmin or SNW1 in the presence of a test compound, and selecting the test compound that inhibits the binding of PPIL1 and stathmin or SNW1.
  • the present application also provides a pharmaceutical composition for treating cell proliferative disease, such as cancer.
  • the pharmaceutical composition may be, for example, an anti-cancer agent.
  • the pharmaceutical composition can be described as at least a portion of the antisense S-oligonucleotides or siRNA of the WDRPUH, KRZFPUH, PPIL1, or APCDD1 polynucleotide sequence shown and described in SEQ ID NO: 1, 3, 5, or 7, respectively.
  • a suitable antisense S-oligonucleotide has the nucleotide sequence selected from the group of SEQ ID NO: 16, 37, 44, or 89.
  • the antisense S-oligonucleotide of WDRPUH including those having the nucleotide sequence of SEQ ID NO: 16 may be suitably used to treat hepatoma, and gastric cancer; the antisense S-oligonucleotide of KRZFPUH including those having the nucleotide sequence of SEQ ID NO: 37 suitably to treat hepatoma, gastric cancer and lung cancer; the antisense S-oligonucleotide of PPIL1 including those having the nucleotide sequence of SEQ ID NO: 44 suitably for colon cancer, and the antisense S-oligonucleotide of APCDD1 including those having the nucleotide sequence of SEQ ID NO: 89 suitably for colorectal carcinoma.
  • the pharmaceutical compositions may be also those comprising the compounds selected by the present methods of screening for compounds for treating cell proliferative diseases.
  • the course of action of the pharmaceutical composition is desirably to inhibit growth of the cancerous cells.
  • the pharmaceutical composition may be applied to mammals including humans and domesticated mammals.
  • the present invention further provides methods for treating a cell proliferative disease using the pharmaceutical composition provided by the present invention.
  • the present invention provides method for treating or preventing cancer, which method comprises the step of administering the WDRPUH, KRZFPUH, PPIL1, or APCDD1 polypeptide. It is expected that anti tumor immunity be induced by the administration of the WDRPUH, KRZFPUH, PPIL1, or APCDD1 polypeptide.
  • the present invention also provides method for inducing anti tumor immunity, which method comprises the step of administering the WDRPUH, KRZFPUH, PPIL1, or APCDD1 polypeptide, as well: as pharmaceutical composition for treating or preventing cancer comprising the WDRPUH KRZFPUH, PPIL1, or APCDD1 polypeptide.
  • FIG. 1 a to 1 d depict the expression of WDRPUH and KRZFPUH in HCCs.
  • FIG. 1 a depicts the relative expression ratios (cancer/non-cancer) of WDRPUH in 20 HCCs examined by cDNA microarray. Its expression was up-regulated (Cy3:Cy5 intensity ratio, >2.0) in 11 of the 12 HCCs that passed through the cutoff filter (both Cy3 and Cy5 signals greater than 25,000).
  • FIG. 1 b depicts the relative expression ratios (cancer/non-cancer) of KRZFPUH in the 20 HCCs. Its expression was up-regulated (Cy3:Cy5 intensity ratio, >2.0) in 11 of the 14 HCCs that passed through the cutoff filter.
  • FIG. 1 c and 1 d present photographs depicting the expression of WDRPUH (c) and KRZFPUH (d) analyzed by semi-quantitative RT-PCR using additional 10 HCC cases (T, tumor tissue; N, normal tissue). Expression of GAPDH served as an internal control.
  • FIG. 2 a and 2 b depict the expression of WDRPUH in various human tissues and the predicted protein structure and protein motifs of WDRPUH.
  • FIG. 2 a is a photograph depicting the expression of WDRPUH in various human tissues analyzed by multiple-tissue northern blot analysis.
  • FIG. 2 b depicts the predicted protein structure of WDRPUH.
  • FIG. 3 is a photograph depicting the sub-cellular localization of WDRPUH observed by immunocytochemistry on SNU475 cells transfected with pcDNA3.1myc/His-WDRPUH, particularly using anti-myc monoclonal antibody and for visualization FITC conjugated secondary anti-mouse IgG antibody. Nuclei were counter-stained with DAPI.
  • FIG. 4 a and 4 b depict the effect of WDRPUH on the cell growth of NIH3T3 cells.
  • FIG. 4 a is a photograph depicting the result of a colony formation assay of NIH3T3 cells transfected with WDRPUH, antisense against WDRPUH, and the vector alone.
  • FIG. 4 b depicts the number of colonies counted by electric densitometry.
  • a (*) denotes a significant difference (p ⁇ 0.05) from control cells as determined by a Student's t test.
  • FIG. 5 a and 5 b depict the growth suppressive effect of antisense S-oligonucleotides designated to suppress WDRPUH.
  • FIG. 5 a presents photographs depicting the expression of WDRPUH and GAPDH (control) in SNU475 cells treated with either sense (WDRPUH-S4) or antisense (WDRPUH-AS4) oligonucleotides for 12 h.
  • FIG. 5 b depict the cell viability of SNU475 cells 72 h after oligonucleotide treatment measured by MTT assay.
  • FIG. 6A and 6B depict the growth suppressive effect of WDRPUH-siRNAs.
  • FIG. 6A presents photographs depicting the expression of WDRPUH and GAPDH (control) in HepG2 cells transfected with WDRPUH-siRNAs.
  • FIG. 6B presents photographs depicting the result of Giemsa's staining of viable cells treated with control-siRNAs or WDRPUH-siRNAs.
  • FIG. 7 is a photograph depicting the result of a Slot blot analysis of FLAG-tagged WDRPUH protein using anti-WDRPUH anti-sera (#1, #2, and #3), pre-immune sera, and anti-FLAG antibody.
  • FIG. 8 a and 8 b depict the expression of KRZFPUH in various human tissues and the predicted protein structure and protein motifs of KRZFPUH.
  • FIG. 8 a is a photograph depicting the expression of KRZFPUH in various human tissues analyzed by multiple-tissue northern blot analysis.
  • FIG. 8 b depicts the predicted protein structure of KRZFPUH.
  • FIG. 9 is a photograph depicting the sub-cellular localization of KRZFPUH observed by immunocytochemistry on SNU475 cells transfected with pcDNA3.1myc/His-KRZFPUH, particularly using anti-His monoclonal antibody and for visualization Rhodamine conjugated secondary anti-mouse IgG antibody. Nuclei were counter-stained with DAPI.
  • FIG. 10 a and 10 b depict the effect of KRZFPUH on the cell growth of COS7 cells.
  • FIG. 10 a is a photograph depicting the result of a colony formation assay of COS7 cells transfected with KRZFPUH, and antisense against KRZFPUH.
  • FIG. 10 b depicts the number of colonies counted by electric densitometry.
  • a (*) denotes a significant difference (p ⁇ 0.05) from control cells as determined by a Student's t test.
  • FIG. 11 a and 11 b depict the growth suppressive effect of antisense S-oligonucleotides designated to suppress KRZFPUH.
  • FIG. 11 a presents photographs depicting the expression of WDRPUH and GAPDH (control) in Alexander cells transfected with sense (KRZFPUH-S4) or antisense (KRZFPUH-AS4) oligonucleotides.
  • FIG. 11 b depicts the expression of KRZFPUH in SNU475 cells treated with either KRZFPUH-S4 or KRZFPUH-AS4 for 12 h.
  • a (*) denotes a significant difference (p ⁇ 0.05) from control cells as determined by a Student's t test.
  • FIG. 12A to 12 D depict the growth suppressive effect of KRZFPUH-siRNAs on the expression of KRZFPUH in Huh7 cells.
  • FIG. 12A depicts the result of semiquantitative RT-PCR carried out using RNA extracted from Huh7 cells transfected with psiU6BX-KRZFPUH2 (Si-02), psiU6BX-EGFP (EGFP), or mock vector (Mock). GAPDH served as an internal control.
  • FIG. 12B depicts the result of MTT assay of viable cells transfected with control plasmid (Mock and EGFP) or plasmids expressing KRZFPUH-siRNAs at Day 5 of transfection.
  • FIG. 12C depicts the result of MTT assay of viable cells transfected with control plasmid (Mock and EGFP) or psiU6BX-KRZFPUH2 (Si-02) at Day 10 of transfection.
  • a (*) denotes a significant difference (p ⁇ 0.01) as determined by a Fisher's protected least significant difference test.
  • 12D presents photographs depicting the result of Giemsa's staining of viable cells transfected with control plasmid (Mock and EGFP) or psiU6BX-KRZFPUH2 (Si-02) at Day 10 of transfection.
  • FIG. 13A to 13 C depict the effect of KRZFPUH-siRNAs on the viability of various cells.
  • FIG. 13A depicts the result of MIT assay carried out using Alexander cells transfected with control plasmid (Mock and EGFP) or psiU6BX-KRZFPUH2 (Si-02) at Day 10 of transfection.
  • FIG. 13B depicts the effect of MTT assay carried out using SNU449 cells transfected with control plasmid (Mock and EGFP) or psiU6BX-KRZFPUH2 (Si-02) at Day 10 of transfection.
  • FIG. 13C depicts the effect of KRZFPUH-siRNAs on the viability of HepG2 cells measured by MTT assay.
  • a (*) denotes significant difference (p ⁇ 0.01) as determined by a Fisher's protected least significant difference test.
  • FIGS. 14 a and 14 b depict the expression of PPIL1 in colon cancer.
  • FIG. 14 a depicts the relative expression ratio (cancer/non-cancer) of PPIL1 in 11 colon cancer cases examined by cDNA microarray. Its expression was up-regulated (Cy3:Cy5 intensity ratio, >2.0) in 6 of the 6 cases that passed through the cutoff filter.
  • FIG. 14 b presents photographs depicting the expression of PPIL1 analyzed by semi-quantitative RT-PCR using additional 20 colon cancer cases (T, tumor tissue; N, normal tissue). Expression of GAPDH served as an internal control.
  • FIG. 15 depicts the similarity between PPIL1 ( Homo sapiens ), Ppil1 ( Mus musculus ), Cyp2 ( Schzosaccharomyces pombe ), and CypE ( Dictiostelium discoideum ).
  • FIG. 16 depicts the effect of PPIL1 on the cell growth of NIH3T3 and HCT116 cells.
  • FIG. 16 a is a photograph depicting the result of a colony formation assay of NIH3T3 cells transfected with PPIL1.
  • FIG. 16 b is a photograph depicting the result of a colony formation assay of HCT 116 cells transfected with PPIL1.
  • pcDNA-LacZ and pcDNA3.1-antisense expressing complementary strand of the coding region of PPIL1 served as negative controls.
  • FIG. 17 a to 17 c depict the growth suppressive effect of antisense S-oligonucleotides of PPIL1 in human colon cancer cell line, SW480.
  • FIG. 17 a presents photographs depicting the expression of PPIL1 and GAPDH (control) in SW480 cells treated with sense (PPIL1-52), antisense (PPIL1-AS2), or scramble (PPIL1-SCR2) S-oligonucleotides.
  • FIG. 17 b is a photograph depicting the growth suppressive effect of PPIL1-AS2.
  • FIG. 17 c depicts the cell viability of SE480, SNUC4, and SNUC5 cells 72 h after oligonucleotides treatment measured by MTT assay.
  • FIG. 18 presents photographs demonstrating that PPIL1 associates with SNW1 in vitro.
  • COS7 cells were cotransfected with pFLAG CMV-PPIL1 and pcDNA3.1myc/His-SNW1. Lysates from the cells were immunoprecipitated with either anti c-Myc polyclonal antibody or anti FLAG monoclonal antibody, and immunoblot was performed with anti-FLAG monoclonal antibody or anti c-Myc polyclonal antibody, respectively.
  • FIG. 19 a to 19 d presents photographs depicting the subcellular localization of FLAG-tagged PPIL1 and myc-tagged SNW1 protein.
  • FIG. 19 a is a photograph of COS7 cells transfected with pFLAG CMV-PPIL1 and stained with anti-FLAG M2 monoclonal antibody. The tagged protein was visualized using anti mouse IgG antibody labeled with Rhodamine.
  • FIG. 19 b is a photograph of COS7 cells transfected with pcDNA3myc/His-SNW1 and stained with anti c-Myc antibody. The tagged protein was visualized by anti rabbit IgG antibody labeled with FITC.
  • FIG. 19 a is a photograph of COS7 cells transfected with pFLAG CMV-PPIL1 and stained with anti-FLAG M2 monoclonal antibody. The tagged protein was visualized using anti mouse IgG antibody labeled with Rhodamine.
  • FIG. 19 b is a photograph of CO
  • FIG. 19 c is a photograph of the cells wherein the nuclei were counter-stained with DAPI.
  • FIG. 19 d is a merged image of (a), (b) and (c). PPIL1 and SNW1 were co-localized in the nucleus.
  • FIG. 20 is a photograph depicting the expression of PPIL1 in various human tissues analyzed by multiple-tissue northern blot analysis.
  • FIG. 21A and 21B depict the growth suppressive effect of PPIL1-siRNAs in SNUC4 and SNUC5 cells.
  • FIG. 21A presents photographs depicting the expression of PPIL1 and GAPDH (control) in SNUC4 and SNUC5 cells transfected with PPIL1-siRNAs.
  • FIG. 21B presents photographs depicting the result of Giemsa's staining of viable cells treated with control-siRNAs or PPIL1-siRNAs.
  • FIG. 22A and 22B depict the expression of PPIL1 recombinant protein in E. coli .
  • FIG. 22A is a photograph depicting the expression of GST-fused PPIL1 protein.
  • FIG. 22B is a photograph depicting the expression of His-tagged PPIL1 protein.
  • FIG. 23A and 23B depict the interaction between PPIL1 and stathmin in yeast two-hybrid system.
  • FIG. 23A is a photograph depicting the interaction of PPIL1 with stathmin in the two-hybrid system.
  • FIG. 23B is a photograph depicting the interaction of PPIL1 with stathmin in vivo.
  • FIG. 24 depict the co-localization of PPIL1 and stathmin in the cytoplasms of COS7 cells co-transfected with pFLAG-PPIL1 and pCMV-HA-STMN.
  • FIG. 24 present photographs depicting the result of fluorescent immunohistochemical staining of PPIL1 and stathmin in the cytoplasms of COS7 cells.
  • FIG. 25A and 25B depict the interaction of various deletion mutants of stathmin with PPIL1 in vivo.
  • FIG. 25A shows schematic illustrations of the structure of various deletion mutants of stathmin.
  • FIG. 25B presents photographs depicting the expression of stathmin and co-precipitation of PPIL1 with the deletion mutants in vivo.
  • FIG. 26A and 26B depict the expression and interaction of mutants of stathmin with PPIL1 in vivo.
  • FIG. 26A shows a schematic illustration of stathmin mutants wherein Ser was substituted with Ala.
  • FIG. 26B presents photographs depicting the expression of stathmin and co-precipitation of PPIL1 with the mutants in vivo.
  • FIG. 27 a to 27 c present photographs showing the expression of APCDD1.
  • FIG. 27 a presents photographs demonstrating the decrease in the expression of APCDD1 in SW480 cells transfected with either Ad-APC or Ad-Axin. RNAs and protein extracts were isolated from the SW480 cells infected with the indicated adenoviruses at MOI100 and incubated for 72 hours.
  • FIG. 27 b is a photograph depicting the expression of APCDD1 in adult human tissues analyzed by Northern blotting. APCDD1 is predominantly expressed in heart, pancreas, prostate and ovary but scarcely expressed in lung, liver, kidney, spleen, thymus, colon, and peripheral blood cells.
  • 27 c presents photo graphs showing the expression of APCDD1 in colon-cancer tissues (T) and corresponding non-cancerous mucosae (N) measured by semiquantitative RT-PCR. Increased expression was observed in 20 of the 30 cases examined (67%). Expression of GAPDH served as the internal control.
  • FIG. 29 is a photograph depicting the result of EMSA showing the interaction between elements containing either TBM1 or TBM2 and the P-catenin/Tcf4 complex.
  • a supershift of the band representing the complex was observed after the addition of anti- ⁇ -catenin antibody (Lane 2) but not with anti-P53-antibody (Lane 3).
  • Bands corresponding to Tcf4-probe and ⁇ -catenin/Tcf4-probe were blocked specifically by the addition of non-labeled wild-type probe (Lane 5).
  • FIG. 30 depicts the effect of APCDD1 on cell growth in LoVo cells in vitro.
  • FIG. 30 a is a photograph showing the result of a colony-formation assay in LoVo cells. The cells were transfected with pcDNA3.1-APCDD1, pcDNA, or pcDNA-antisense.
  • FIG. 30 b is a photograph demonstrating the expression of APCDD1 in LoVo, cells that express exogenous APCDD1 (LoVo-APCDD1) and control (LoVo-vector) cells.
  • FIG. 30 c depicts the growth of LoVo-APCDD1 and LoVo-vector cells.
  • FIG. 30 d depicts the growth of tumor in two clones of LoVo-APCDD1 cells and two clones of LoVo-vector cells in nude mice.
  • FIG. 31A to 31 C depict the growth inhibitory effect of antisense S-oligonucleotides designated to reduce the expression of APCDD1.
  • FIG. 31A presents photographs depicting the expression of APCDD1 in SW480 cells treated with sense (APCDD-S2) or antisense (APCDD-AS2) S-oligonucleotides for 24 hours. The expression of GAPDH served as an internal control.
  • FIG. 31B is a photograph depicting the growth suppressive effect of APCDD-AS2.
  • FIG. 31C depicts the cell viability of SW480 cells after oligonucleotide treatment measured by MIT assay. Bars, SD.
  • a (*) denotes significant difference (P ⁇ 0.01) as determined by a Scheffé's F test.
  • FIG. 32 is a photograph demonstrating the result of Western blot analysis of COS7 cells transfected with APCDD1 and with or without pFLAG-APCDD1, and colon cancer cell lines.
  • FIG. 33 presents photographs depicting the subcellular localization of APCDD1 protein in SW480 cells.
  • FIG. 34 presents photographs depicting the result of fluorescent immunohistochemical staining of APCDD1 in non-cancerous mucosa (A) and adenocarcinoma (B) of the colon.
  • FIG. 35 presents photographs depicting the result of immunohistochemical staining of APCDD1 in colon cancer tissues.
  • FIG. 36 presents photographs depicting the result of immunohistochemical staining of APCDD1 in adenomas of colon.
  • the present application identifies novel human genes WDRPUH and KRZFPUH whose expression is markedly elevated in HCCs compared to corresponding non-cancerous liver tissues.
  • the WDRPUH cDNA consists of 2152 nucleotides that contain an open reading frame of 1860 nucleotides as set forth in SEQ ID NO: 1.
  • the open reading frame encodes a putative 620-amino acid protein with 11 WD40 repeats domains. Therefore this protein has been named WDRPUH (WD40 repeats protein up-regulated in HCCs).
  • the KRZFPUH cDNA consists of 2744 nucleotides that contain an open reading frame of 1500 nucleotides as set forth in SEQ ID NO: 3.
  • the open reading frame encodes a putative 500-amino acid protein containing a Kruppel-type zinc finger domain. Therefore this protein has been named KRZFPUH (Krupple-type zinc finger protein up-regulated in HCCs).
  • the present invention encompasses novel human genes PPIL1 and APCDD1 whose expression is markedly elevated in colorectal cancer compared to corresponding non-cancerous tissue.
  • the PPIL1 cDNA consists of 1734 nucleotides that contain an open reading frame of 498 nucleotides as set forth in SEQ ID NO: 5. The open reading frame encodes a putative: 166-amino acid protein.
  • PPIL1 directly associates with a SKI interacting protein (SNW1), a protein involved in transcriptional activity of vitamin D receptor, and stathmin, a cytosolic phosphorprotein involved in the progression of the cell cycle.
  • SKI interacting protein SNW1
  • stathmin a cytosolic phosphorprotein involved in the progression of the cell cycle.
  • the APCDD1 cDNA consists of 2607 nucleotides that contain an open reading frame of 1542 nucleotides as set forth in SEQ ID NO: 7.
  • the open reading frame encodes a putative 514-amino acid protein with no known motif.
  • the gene was dubbed APCDD1 (down-regulated by APC 1).
  • the expression of APCDD1′ is enhanced by the ⁇ -catenin/Tcf 4 complex through the binging of the complex to the two Tcf/LEF binding motifs in the transcriptional regulatory region of APCDD1.
  • the present invention encompasses novel human gene WDRPUH, including a polynucleotide sequence as described in SEQ ID NO: 1, as well as degenerates and mutants thereof, to the extent that they encode a WDRPUH protein, including the amino acid sequence set forth in SEQ ID NO: 2 or its functional equivalent.
  • WDRPUH includes, for example, homologous proteins of other organisms corresponding to the human WDRPUH protein; as well as mutants of human WDRPUH proteins.
  • the present invention also encompasses novel human gene KRZFPUH, including a polynucleotide sequence as described in SEQ ID NO: 3, as well as degenerates and mutants thereof, to the extent that they encode a KRZFPUH protein, including the amino acid sequence set forth in SEQ ID NO: 4 or its functional equivalent.
  • polypeptides functionally equivalent to KRZFPUH include, for example, homologous proteins of other organisms corresponding to the human KRZFPUH protein, as well as mutants of human KRZFPUH proteins.
  • the present invention encompasses novel human gene PPIL1, including a polynucleotide sequence as described in SEQ ID NO: 5, as well as degenerates and mutants thereof, to the extent that they encode a PPIL1 protein, including the amino acid sequence set forth in SEQ ID NO: 6 or its functional equivalent.
  • polypeptides functionally equivalent to PPIL1 include, for example, homologous proteins of other organisms corresponding to the human PPIL1 protein, as well as mutants of human PPIL1 proteins.
  • the present invention further encompasses novel human gene APCDD1, including a polynucleotide sequence as described in SEQ ID NO: 7, as well as degenerates and mutants thereof, to the extent that they encode a APCDD1 protein, including the amino acid sequence set forth in SEQ ID NO: 8 or its functional equivalent.
  • APCDD1 includes, for example, homologous proteins of other organisms corresponding to the human APCDD1 protein, as well as mutants of human APCDD1 proteins.
  • the term “functionally equivalent” means that the subject polypeptide has the activity to promote cell proliferation like WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein and to confer oncogenic activity to cancer cells. Whether the subject polypeptide has a cell proliferation activity or not can be judged by introducing a DNA encoding the subject polypeptide into a cell expressing the respective polypeptide, and detecting promotion of proliferation of the cells or increase in colony forming activity.
  • Such cells include, for example, NIH3T3, SNU475, and HepG2 for WDRPUH; COS7, and Alexander cells for KRZFPUH; NIH313, HCl 116, SW480, SNU-C4, and SNU-C5 for PPIL1; and LoVo cells, and SW480 for APCDD1.
  • whether the subject polypeptide is functionally equivalent to PPIL1 may be judged by detecting its binding ability to SNW1 or stathmin.
  • polypeptides functionally equivalent to a given protein are well known by a person skilled in the art and include known methods of introducing mutations into the protein.
  • one skilled in the art can prepare polypeptides functionally equivalent to the human WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein by introducing an appropriate mutation in the amino acid sequence of either of these proteins by site-directed mutagenesis (Hashimoto-Gotoh et al., Gene 152: 271-275 (1995); Zoller and Smith, Methods Enzymol 100: 468-500 (1983); Kramer et al., Nucleic Acids Res.
  • the polypeptide of the present invention includes those proteins having the amino acid sequences of the human WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein in which one or more amino acids are mutated, provided the resulting mutated polypeptides are functionally equivalent to the human WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein.
  • the number of amino acids to be mutated in such a mutant is generally 10 amino acids or less, preferably 6 amino acids or less, and more preferably 3 amino acids or less.
  • Mutated or modified proteins proteins having amino acid sequences modified by substituting, deleting, inserting, and/or adding one or more amino acid residues of a certain amino acid sequence, have been known to retain the original biological activity (Mark et al., Proc Natl Acad Sci USA 81: 5662-5666 (1984); Zoller and Smith, Nucleic Acids Res 10: 6487-6500(1982); Dalbadie-McFarland et al., Proc Natl Acad Sci USA 79: 6409-6413 (1982)).
  • the amino acid residue to be mutated is preferably mutated into a different amino acid in which the properties of the amino acid side-chain are conserved (a process known as conservative amino acid substitution).
  • properties of amino acid side chains are hydrophobic amino acids (A, I, L, M, F, P, W, Y, V), hydrophilic amino acids (R, D, N, C, E, Q, G, H, K, S, T), and side chains having the following functional groups or characteristics in common: an aliphatic side-chain (G, A, V, L, P); a hydroxyl group containing side-chain (S, T, Y); a sulfur atom containing side-chain (C, M); a carboxylic acid and amide containing side-chain (D, N, E, Q); a base containing side-chain (R, K, H); and an aromatic containing side-chain (H, F, Y, W).
  • the parenthetic letters indicate the one-letter codes of amino acids.
  • polypeptide to which one or more amino acids residues are added to the amino acid sequence of human WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein is a fusion protein containing the human WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein. Fusion proteins are, fusions of the human WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein and other peptides or proteins, and are included in the present invention.
  • Fusion proteins can be made by techniques well known to a person skilled in the art, such as by linking the DNA encoding the human WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein of the invention with DNA encoding other peptides or proteins, so that the frames match, inserting the fusion DNA into an expression vector and expressing it in a host. There is no restriction as to the peptides or proteins fused to the protein of the present invention.
  • peptides that can be used as peptides that are fused to the protein of the present invention include, for example, FLAG (Hopp et al., Biotechnology 6: 1204-1210 (1988)), 6 ⁇ His containing six His (histidine) residues, 10 ⁇ His, Influenza agglutinin (HA), human c-myc fragment, VSP-GP fragment, p18HIV fragment, T7-tag, HSV-tag, E-tag, SV40T antigen fragment, lck tag, ⁇ -tubulin fragment, B-tag, Protein C fragment, and the like.
  • FLAG Hopp et al., Biotechnology 6: 1204-1210 (1988)
  • 6 ⁇ His containing six His (histidine) residues 10 ⁇ His
  • Influenza agglutinin (HA) Influenza agglutinin
  • human c-myc fragment VSP-GP fragment
  • p18HIV fragment T7-tag
  • HSV-tag HSV-tag
  • Fusion proteins can be prepared by fusing commercially available DNA, encoding the fusion peptides or proteins discussed above, with the DNA encoding the polypeptide of the present invention and expressing the fused DNA prepared.
  • polypeptides of the present invention include those that are encoded by DNA that hybridize with a whole or part of the DNA sequence encoding the human WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein and are functionally equivalent to the human WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein.
  • These polypeptides include mammal homologues corresponding to the protein derived from human (for example, a polypeptide encoded by a monkey, rat, rabbit, and bovine gene). In isolating a cDNA highly homologous to the DNA encoding the human WDRPUH protein from animals, it is particularly preferable to use tissues from testis.
  • tissue from placenta or testis in isolating a cDNA highly homologous to the DNA encoding the human KRZFPUH from animals, it is particularly preferable to use tissues from placenta or testis.
  • tissues from heart, skeletal muscle, testis, thyroid, or adrenal gland in isolating that to the DNA encoding the human APCDD1 protein, preferably tissue from heart, pancreas, prostate, ovary, lung, liver, kidney, spleen, thymus, colon, or peripheral leukocyte, and particularly preferably tissue from heart, pancreas, prostate, or ovary is used.
  • hybridization for isolating a DNA encoding a polypeptide functionally equivalent to the human WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein can be routinely selected by a person skilled in the art.
  • hybridization may be performed by conducting prehybridization at 68° C. for 30 min or longer using “Rapid-hyb buffer” (Amersham LIFE SCIENCE), adding a labeled probe, and warming at 68° C. for 1 hour or longer.
  • the following washing step can be conducted, for example, in a low stringent condition.
  • a low stringent condition is, for example, 42° C., 2 ⁇ SSC, 0.1% SDS, or preferably 50° C., 2 ⁇ SSC, 0.1% SDS. More preferably, high stringent conditions are used.
  • a high stringent condition is, for example, washing 3 times in 2 ⁇ SSC, 0.01% SDS at room temperature for 20 min, then washing 3 times in 1 ⁇ SSC, 0.1% SDS at 37° C. for 20 min, and washing twice in 1 ⁇ SSC, 0.1% SDS at 50° C. for 20 min.
  • factors such as temperature and salt concentration, can influence the stringency of hybridization and one skilled in the art can suitably select the factors to achieve the requisite stringency.
  • a gene amplification method for example, the polymerase chain reaction (PCR) method, can be utilized to isolate a DNA encoding a polypeptide functionally equivalent to the human WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein, using a primer synthesized based on the sequence information of the protein encoding DNA (SEQ ID NO: 1, 3, 5, or 7).
  • PCR polymerase chain reaction
  • Polypeptides that are functionally equivalent to the human WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein encoded by the DNA isolated through the above hybridization techniques or gene amplification techniques normally have a high homology to the amino acid sequence of the human WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein.
  • “High homology” typically refers to a homology of 40% or higher, preferably 60% or higher, more preferably 80% or higher, even more preferably 95% or higher.
  • the homology of a polypeptide can be determined by following the algorithm in “Wilbur and Lipman, Proc Nat Acad Sci USA 80:726-730 (1983)”.
  • a polypeptide of the present invention may have variations in amino acid sequence, molecular weight, isoelectric point, the presence or absence of sugar chains, or form, depending on the cell or host used to produce it or the purification method utilized.
  • polypeptides of the present invention can be prepared as recombinant proteins or natural proteins, by methods well known to those skilled in the art.
  • a recombinant protein can be prepared by inserting a DNA, which encodes the polypeptide of the present invention (for example, the DNA comprising the nucleotide sequence of SEQ ID NO: 1, 3, 5, or 7), into an appropriate expression vector, introducing the vector into an appropriate host cell, obtaining the extract, and purifying the polypeptide by subjecting the extract to chromatography, for example, ion exchange chromatography, reverse phase chromatography, gel filtration, or affinity chromatography utilizing a column to which antibodies against the protein of the present invention is fixed, or by combining more than one of aforementioned columns.
  • chromatography for example, ion exchange chromatography, reverse phase chromatography, gel filtration, or affinity chromatography utilizing a column to which antibodies against the protein of the present invention is fixed, or by combining more than one of aforementioned columns.
  • polypeptide of the present invention when expressed within host cells (for example, animal cells and E. Coli ) as a fusion protein with glutathione-S-transferase protein or as a recombinant protein supplemented with multiple histidines, the expressed recombinant protein can be purified using a glutathione column or nickel column.
  • host cells for example, animal cells and E. Coli
  • the polypeptide of the present invention is expressed as a protein tagged with c-myc, multiple histidines, or FLAG, it can be detected and purified using antibodies to c-myc, His, or FLAG, respectively.
  • a natural protein can be isolated by methods known to a person skilled in the art, for example, by contacting the affinity column, in which antibodies binding to the WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein described below are bound, with the extract of tissues or cells expressing the polypeptide of the present invention.
  • the antibodies can be polyclonal antibodies or monoclonal antibodies.
  • the present invention also encompasses partial peptides of the polypeptide of the present invention.
  • the partial peptide has an amino acid sequence specific to the polypeptide of the present invention and consists of at least 7 amino acids, preferably 8 amino acids or more, and more preferably 9 amino acids or more.
  • the partial peptide can be used, for example, for preparing antibodies against the polypeptide of the present invention, screening for a compound that binds to the polypeptide of the present invention, and screening for accelerators or inhibitors of the polypeptide of the present invention.
  • a partial peptide of the invention can be produced by genetic engineering, by known methods of peptide synthesis, or by digesting the polypeptide of the invention with an appropriate peptidase.
  • peptide synthesis for example, solid phase synthesis or liquid phase synthesis may be used.
  • the present invention provides polynucleotides encoding the polypeptide of the present invention.
  • the polynucleotides of the present invention can be used for the in vivo or in vitro production of the polypeptide of the present invention as described above, or can be applied to gene therapy for diseases attributed to genetic abnormality in the gene encoding the protein of the present invention.
  • Any form of the polynucleotide of the present invention can be used so long as it encodes the polypeptide of the present invention, including mRNA, RNA, cDNA, genomic DNA, chemically synthesized polynucleotides.
  • the polynucleotide of the present invention include a DNA comprising given nucleotide sequences as well as its degenerate sequences, so long as the resulting DNA encodes a polypeptide of the present invention.
  • the polynucleotide of the present invention can be prepared by methods known to a person skilled in the art.
  • the polynucleotide of the present invention can be prepared by: preparing a cDNA library from cells which express the polypeptide of the present invention, and conducting hybridization using a partial sequence of the DNA of the present invention (for example, SEQ ID NO: 1, 3, 5, or 7) as a probe.
  • a cDNA library can be prepared, for example, by the method described in Sambrook et al., Molecular Cloning, Cold Spring Harbor Laboratory Press (1989); alternatively, commercially available cDNA libraries may be used.
  • a cDNA library can be also prepared by: extracting RNAs from cells expressing the polypeptide of the present invention, synthesizing oligo DNAs based on the sequence of the DNA of the present invention (for example, SEQ ID NO: 1, 3, 5, or 7), conducting PCR using the oligo DNAs as primers, and amplifying cDNAs encoding the protein of the present invention.
  • the translation region encoded by the cDNA can be routinely determined, and the amino acid sequence of the polypeptide of the present invention can be easily obtained.
  • the genomic DNA library using the obtained cDNA or parts thereof as a probe, the genomic DNA can be isolated.
  • mRNAs may first be prepared from a cell, tissue, or organ (e.g., testis for WDRPUH; placenta or testis for KRZFPUH; heart, skeletal muscle, testis, thyroid, or adrenal gland for PPIL1; and heart, pancreas, prostate, ovary, lung, liver, kidney, spleen, thymus, colon, or peripheral leukocyte, preferably, heart, pancreas, prostate, or ovary for APCDD1) in which the object polypeptide of the invention is expressed.
  • a cell, tissue, or organ e.g., testis for WDRPUH; placenta or testis for KRZFPUH; heart, skeletal muscle, testis, thyroid, or adrenal gland for PPIL1; and heart, pancreas, prostate, ovary, lung, liver, kidney, spleen, thymus, colon, or peripheral leukocyte, preferably, heart, pancreas, prostate, or ovary for APC
  • RNA may be prepared by the guanidine ultracentrifugation (Chirgwin et al., Biochemistry 18: 52945299 (1979)) or the AGPC method (Chomczynski and Sacchi, Anal Biochem 162: 156-159 (1987)).
  • mRNA may be purified from total RNA using mRNA Purification Kit (Pharmacia) and such or, alternatively, mRNA may be directly purified by QuickPrep mRNA Purification Kit (Pharmacia).
  • cDNA is used to synthesize cDNA using reverse transcriptase.
  • cDNA may be synthesized using a commercially available kit, such as the AMV Reverse Transcriptase First-strand cDNA Synthesis Kit (Seikagaku Kogyo).
  • cDNA may be synthesized and amplified following the 5′-RACE method (Frohman et al., Proc Natl Acad Sci USA 85: 8998-9002 (1988); Belyavsky et al., Nucleic Acids Res 17: 2919-2932 (1989)), which uses a primer and such, described herein, the 5′-Ampli FINDER RACE Kit (Clontech), and polymerase chain reaction (PCR).
  • 5′-RACE method Frohman et al., Proc Natl Acad Sci USA 85: 8998-9002 (1988); Belyavsky et al., Nucleic Acids Res 17: 2919-2932 (1989
  • a desired DNA fragment is prepared from the PCR products and ligated with a vector DNA.
  • the recombinant vectors are used to transform E. coli and such, and a desired recombinant vector is prepared from a selected, colony.
  • the nucleotide sequence of the desired DNA can be verified by conventional methods, such as dideoxynucleotide chain termination.
  • the nucleotide sequence of a polynucleotide of the invention may be designed to be expressed more efficiently by taking into account the frequency of codon usage in the host to be used for expression (Grantham et al., Nucleic Acids Res 9: 43-74 (1981)).
  • the sequence of the polynucleotide of the present invention may be altered by a commercially available kit or a conventional method. For instance, the sequence may be altered by digestion with restriction enzymes, insertion of a synthetic oligonucleotide or an appropriate polynucleotide fragment, addition of a linker, or insertion of the initiation codon (ATG) and/or the stop codon (TAA, TGA, or TAG).
  • polynucleotide of the present invention encompasses the DNA comprising the nucleotide sequence of SEQ ID NO: 1, 3, 5, or 7.
  • the present invention provides a polynucleotide that hybridizes under stringent conditions with a polynucleotide having a nucleotide sequence of SEQ ID NO: 1, 3, 5, or 7, and encodes a polypeptide functionally equivalent to the WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein of the invention described above.
  • stringent conditions For example, low stringent condition can be used. More preferably, high stringent condition can be used. These conditions are the same as that described above.
  • the hybridizing DNA above is preferably a cDNA or a chromosomal DNA.
  • the present invention also provides a vector into which a polynucleotide of the present invention is inserted.
  • a vector of the present invention is useful to keep a polynucleotide, especially a DNA, of the present invention in host cell, to express the polypeptide of the present invention, or to administer the polynucleotide of the present invention for gene therapy.
  • E. coli When E. coli is a host cell and the vector is amplified and produced in a large amount in E. coli (e.g., JM109, DH5 ⁇ , HB101, or XL1Blue), the vector should have “ori” to be amplified in E. coli and a marker gene for selecting transformed E. coli (e.g., a drug-resistance gene selected by a drug such as ampicillin, tetracycline, kanamycin, chloramphenicol or the like).
  • a marker gene for selecting transformed E. coli e.g., a drug-resistance gene selected by a drug such as ampicillin, tetracycline, kanamycin, chloramphenicol or the like.
  • M13-series vectors, pUC-series vectors, pBR322, pBluescript, pCR-Script, etc. can be used.
  • pGEM-T pDIRECT, and pT7 can also be used for subcloning land extracting cDNA as well as the vectors described above.
  • an expression vector is especially useful.
  • an expression vector to be expressed in E. coli should have the above characteristics to be amplified in E. coli .
  • the vector should have a promoter, for example, lacZ promoter (Ward et al., Nature 341: 544-546 (1989); FASEB J 6:2422-2427 (1992)), araB promoter (Better et al., Science 240: 1041-1043 (1988)), or T7 promoter or the like, that can efficiently express the desired gene in E. coli .
  • a promoter for example, lacZ promoter (Ward et al., Nature 341: 544-546 (1989); FASEB J 6:2422-2427 (1992)), araB promoter (Better et al., Science 240: 1041-1043 (1988)), or T7 promoter or the like, that can efficiently express the desired gene in E. coli .
  • pGEX-5 ⁇ -1 Pulacia
  • QIAexpress system (Qiagen)
  • pEGFP pEGFP
  • pET pET
  • the host is preferably BL21 which expresses T7 RNA-polymerase
  • the vector may also contain a signal sequence for polypeptide secretion.
  • An exemplary signal sequence that directs the polypeptide to be secreted to the periplasm of the E. coli is the pelB signal sequence (Lei et al., J Bacteriol 169: 4379 (1987)).
  • Means for introducing of the vectors into the target host cells include, for example, the calcium chloride method, and the electroporation method.
  • E. coli for example, expression vectors derived from mammals (for example, pcDNA3 (Invitrogen) and pEGF-BOS (Nucleic Acids Res 18(17): 5322 (1990)), pEF, pCDM8), expression vectors derived from insect cells (for example, “Bac-to-BAC baculovirus expression system”(GIBCO BRL), pBacPAK8), expression vectors derived from plants (e.g.
  • pMH1, pMH2 expression vectors derived from animal viruses (e.g., pHSV, pMV, pAdexLcw), expression vectors derived from retroviruses (e.g., pZIpneo), expression vector derived from yeast (e.g., “Pichia Expression Kit” (Invitrogen), pNV11, SP-Q01), and expression vectors derived from Bacillus subtilis (e.g., pPL608, pKTH50) can be used for producing the polypeptide of the present invention.
  • animal viruses e.g., pHSV, pMV, pAdexLcw
  • retroviruses e.g., pZIpneo
  • yeast e.g., “Pichia Expression Kit” (Invitrogen)
  • pNV11, SP-Q01 expression vectors derived from Bacillus subtilis
  • Bacillus subtilis e.g., pPL608, pKTH
  • the vector In order to express the vector in animal cells, such as CHO, COS, or NIH3T3 cells, the vector should have a promoter necessary for expression in such cells, for example, the SV40 promoter (Mulligan et al., Nature 277:108 (1979)), the MMLV-LTR promoter, the EF1 ⁇ promoter (Mizushima et al., Nucleic Acids Res 18:5322 (1990)), the CMV promoter, and the like, and preferably a marker gene for selecting transformants (for example, a drug resistance gene selected by a drug (e.g., neomycin, G418)).
  • a promoter necessary for expression in such cells for example, the SV40 promoter (Mulligan et al., Nature 277:108 (1979)), the MMLV-LTR promoter, the EF1 ⁇ promoter (Mizushima et al., Nucleic Acids Res 18:5322 (1990)), the
  • a vector comprising the complementary DHFR gene may be introduced into CHO cells in which the nucleic acid synthesizing pathway is deleted, and then amplified by methotrexate (MTX).
  • MTX methotrexate
  • the method wherein a vector comprising a replication origin of SV40 (pcD, etc.) is transformed into COS cells comprising the SV40 T antigen expressing gene on the chromosome can be used.
  • a polypeptide of the present invention obtained as above may be isolated from inside or outside (such as medium) of host cells, and purified as a substantially pure homogeneous polypeptide.
  • substantially pure as used herein in reference to a given polypeptide means that the polypeptide is substantially free from other biological macromolecules.
  • the substantially pure polypeptide is at least 75% (e.g., at least 80, 85, 95, or 99%) pure by dry weight. Purity can be measured by any appropriate standard method, for example by column chromatography, polyacrylamide gel electrophoresis, or HPLC analysis. The method for polypeptide isolation and purification is not limited to any specific method; in fact, any standard method may be used.
  • column chromatography filter, ultrafiltration, salt precipitation, solvent precipitation, solvent extraction, distillation, immunoprecipitation, SDS-polyacrylamide gel electrophoresis, isoelectric point electrophoresis, dialysis, and recrystallization may be appropriately selected and combined to isolate and purify the polypeptide.
  • chromatography examples include, for example, affinity chromatography, ion-exchange chromatography, hydrophobic chromatography, gel filtration, reverse phase chromatography, adsorption chromatography, and such (Strategies for Protein Purification and Characterization: A Laboratory Course Manual. Ed. Daniel R. Marshak et al., Cold Spring Harbor Laboratory Press (1996)). These chromatographies may be performed by liquid chromatography, such as HPLC and FPLC. Thus, the present invention provides for highly purified polypeptides prepared by the above methods.
  • a polypeptide of the present invention may be optionally modified or partially deleted by treating it with an appropriate protein modification enzyme before or after purification.
  • useful protein modification enzymes include, but are not limited to, trypsin, chymotrypsin, lysylendopeptidase, protein kinase, glucosidase, and so on.
  • the present invention provides an antibody that binds to the polypeptide of the invention.
  • the antibody of the invention can be used in any form, such as monoclonal or polyclonal antibodies, and includes antiserum obtained by immunizing an animal such as a rabbit with the polypeptide of the invention, all classes of polyclonal and monoclonal antibodies, human-antibodies, and humanized antibodies produced by genetic recombination.
  • a polypeptide of the invention used as an antigen to obtain an antibody may be derived from any animal species, but preferably is derived from a mammal such as a human, mouse, or rat, more preferably from a human.
  • a human-derived polypeptide may be obtained from the nucleotide or amino acid sequences disclosed herein.
  • the polypeptide to be used as an immunization antigen may be a complete protein or a partial peptide of the protein.
  • a partial peptide may comprise, for example, the amino (N)-terminal or carboxy (C)-terminal fragment of a polypeptide of the present invention.
  • an antibody is defined as a protein that reacts with either the full length or a fragment of a polypeptide of the present invention.
  • a gene encoding a polypeptide of the invention or its fragment may be inserted into a known expression vector, which is then used to transform a host cell as described herein.
  • the desired polypeptide or its fragment may be recovered from the outside or inside of host cells by any standard method, and may subsequently be used as an antigen.
  • whole cells expressing the polypeptide or their lysates, or a chemically synthesized polypeptide may be used as the antigen.
  • Any mammalian animal may be immunized with the antigen, but preferably the compatibility with parental cells used for cell fusion is taken into account.
  • animals of Rodentia, Lagomorpha, or Primates are used.
  • Animals of Rodentia include, for example, mouse, rat, and hamster.
  • Animals of Lagomorpha include, for example, rabbit.
  • Animals of Primates include, for example, a monkey of Catarrhini (old world monkey) such as Macaca fascicularis , rhesus monkey, sacred baboon, and chimpanzees.
  • antigens may be diluted and suspended in an appropriate amount of phosphate buffered saline (PBS), physiological saline, etc.
  • PBS phosphate buffered saline
  • the antigen suspension may be mixed with an appropriate amount of a standard adjuvant, such as Freund's complete adjuvant, made into emulsion, and then administered to mammalian animals.
  • a standard adjuvant such as Freund's complete adjuvant
  • an appropriately amount of Freund's incomplete adjuvant every 4 to 21 days.
  • An appropriate carrier may also be used for immunization.
  • serum is examined by a standard method for an increase in the amount of desired antibodies.
  • Polyclonal antibodies against the polypeptides of the present invention may be prepared by collecting blood from the immunized mammal examined for the increase of desired antibodies in the serum, and by separating serum from the blood by any conventional method.
  • Polyclonal antibodies include serum containing the polyclonal antibodies, as well as the fraction containing the polyclonal antibodies may be isolated from the serum.
  • Immunoglobulin G or M can be prepared from a fraction which recognizes only the polypeptide of the present invention using, for example, an affinity column coupled with the polypeptide of the present invention, and further purifying this fraction using protein A or protein G column.
  • immune cells are collected from the mammal immunized with the antigen and checked for the increased level of desired antibodies in the serum as described above, and are subjected to cell fusion.
  • the immune cells used for cell fusion are preferably obtained from spleen.
  • Other preferred parental cells to be fused with the above immunocyte include, for example, myeloma cells of mammalians, and more preferably myeloma cells having an acquired property for the selection of fused cells by drugs.
  • the above immunocyte and myeloma cells can be fused according to known methods, for example, the method of Milstein et al. (Galfre and Milstein, Methods Enzymol 73: 3-46 (1981)).
  • Resulting hybridomas obtained by the cell fusion may be selected by cultivating them in a standard selection medium, such as HAT medium (hypoxanthine, aminopterin, and thymidine containing medium).
  • HAT medium hyperxanthine, aminopterin, and thymidine containing medium.
  • the cell culture is typically continued in the HAT medium for several days to several weeks, the time being sufficient to allow all the other cells, with the exception of the desired hybridoma (non-fused cells), to die. Then, the standard limiting dilution is performed to screen and clone a hybridoma cell producing the desired antibody.
  • human lymphocytes such as those infected by EB virus may be immunized with a polypeptide, polypeptide expressing cells, or their lysates in vitro. Then, the immunized lymphocytes are fused with human-derived myeloma cells that are capable of indefinitely dividing, such as U266, to yield a hybridoma producing a desired human antibody that is able to bind to the polypeptide (Unexamined Published Japanese Patent Application No. (JP-A) Sho 63-17688).
  • JP-A Japanese Patent Application No.
  • the obtained hybridomas are subsequently transplanted into the abdominal cavity of a mouse and the ascites are extracted.
  • the obtained monoclonal antibodies can be purified by, for example, ammonium sulfate precipitation, a protein A or protein G column, DEAE ion exchange chromatography, or an affinity column to which the polypeptide of the present invention is coupled.
  • the antibody of the present invention can be used not only for purification and detection of the polypeptide of the present invention, but also as a candidate for agonists and antagonists of the polypeptide of the present invention.
  • this antibody can be applied to the antibody treatment for diseases related to the polypeptide of the present invention.
  • a human antibody or a humanized antibody is preferable for reducing immunogenicity.
  • transgenic animals having a repertory of human antibody genes may be immunized with an antigen selected from a polypeptide, polypeptide expressing cells, or their lysates.
  • Antibody producing cells are then collected from the animals and fused with myeloma cells to obtain hybridoma, from which human antibodies against the polypeptide can be prepared (see WO92-03918, WO93-2227, WO94-02602, WO94-25585, WO96-33735, and WO96-34096).
  • an immune cell such as an immunized lymphocyte, producing antibodies may be immortalized by an oncogene and used for preparing monoclonal antibodies.
  • Monoclonal antibodies thus obtained can be also recombinantly prepared using genetic engineering techniques (see, for example, Borrebaeck and Larrick, Therapeutic Monoclonal Antibodies, published in the United Kingdom by MacMillan Publishers LTD (1990)).
  • a DNA encoding an antibody may be cloned from an immune cell, such as a hybridoma or an immunized lymphocyte producing the antibody, inserted into an appropriate vector, and introduced into host cells to prepare a recombinant antibody.
  • the present invention also provides recombinant antibodies prepared as described above.
  • an antibody of the present invention may be a fragment of an antibody or modified antibody, so long as it binds to one or more of the polypeptides of the invention.
  • the antibody fragment may be Fab, F(ab′) 2 , Fv, or single chain Fv (scFv), in which Fv fragments from H and L chains are ligated by an appropriate linker (Huston et al., Proc Natl Acad Sci USA 85:5879-5883 (1988)). More specifically, an antibody fragment may be generated by treating an antibody with an enzyme, such as papain or pepsin.
  • a gene encoding the antibody fragment may be constructed, inserted into an expression vector, and expressed in an appropriate host cell (see, for example, Co et al., J Immunol 152: 2968-2976 (1994); Better and Horwitz, Methods Enzymol 178:476-496 (1989); Pluckthun and Skerra, Methods Enzymol 178: 497-515 (1989); Lamoyi, Methods Enzymol. 121:652-663 (1986); Rousseaux et al., Methods Enzymol 121: 663-669 (1986); Bird and Walker, Trends Biotechnol 9:132-137 (1991)).
  • An antibody may be modified by conjugation with a variety of molecules, such as polyethylene glycol (PEG).
  • PEG polyethylene glycol
  • the present invention provides for such modified antibodies.
  • the modified antibody can be obtained by chemically modifying an antibody. These modification methods are conventional in the field.
  • an antibody of the present invention may be obtained as a chimeric antibody, between a variable region derived from nonhuman antibody and the constant region derived from human antibody, or as a humanized antibody, comprising the complementarity determining region (CDR) derived from nonhuman antibody, the frame work region (FR) derived from human antibody, and the constant region.
  • CDR complementarity determining region
  • FR frame work region
  • Antibodies obtained as above may be purified to homogeneity.
  • the separation and purification of the antibody can be performed according to separation and purification methods used for general proteins.
  • the antibody may be separated and isolated by the appropriately selected and combined use of column chromatographies, such as affinity chromatography, filters ultrafiltration, salting-out, dialysis, SDS polyacrylamide gel electrophoresis, isoelectric focusing, and others (Antibodies: A Laboratory Manual. Ed Harlow and David Lane, Cold Spring Harbor Laboratory, 1988), but are not limited thereto.
  • a protein A column and a protein G column can be used as the affinity column.
  • Exemplary protein A columns to be used include, for, example, Hyper D, POROS, and Sepharose F. F. (Pharmacia).
  • Exemplary chromatography with the exception of affinity includes, for example, ion-exchange chromatography, hydrophobic chromatography, gel filtration, reverse-phase chromatography, adsorption chromatography, and the like (Strategies for Protein Purification and Characterization: A Laboratory Course Manual. Ed Daniel R. Marshak et al., Cold Spring Harbor Laboratory Press (1996)).
  • the chromatographic procedures can be carried out by liquid-phase chromatography, such as: HPLC, and FPLC.
  • ELISA enzyme-linked immunosorbent assay
  • EIA enzyme immunoassay
  • RIA radioimmunoassay
  • the antibody of the present invention is immobilized on a plate, a polypeptide of the invention is applied to the plate, and then a sample containing a desired antibody, such as culture supernatant of antibody producing cells or purified antibodies, is applied. Then, a secondary antibody that recognizes the primary antibody and is labeled with an enzyme, such as alkaline phosphatase, is applied, and the plate is incubated.
  • a desired antibody such as culture supernatant of antibody producing cells or purified antibodies
  • an enzyme substrate such as p-nitrophenyl phosphate
  • the absorbance is measured to evaluate the antigen binding activity of the sample.
  • a fragment of the polypeptide such as a C-terminal or N-terminal fragment, may be used as a polypeptide.
  • BIAcore Pharmacia
  • the above methods allow for the detection or measurement of the polypeptide of the invention, by exposing the antibody of the invention to a sample assumed to contain the polypeptide of the invention, and detecting or measuring the immune complex formed by the antibody and the polypeptide.
  • the method of detection or measurement of the polypeptide according to the invention can specifically detect or measure a polypeptide, the method may be useful in a variety of experiments in which the polypeptide is used.
  • the present invention also provides a polynucleotide which hybridizes with the polynucleotide encoding human WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein (SEQ ID NO: 1, 3, 5, or 7) or the complementary strand thereof, and which comprises at least 15 nucleotides.
  • the polynucleotide of the present invention is preferably a polynucleotide which specifically hybridizes with the DNA encoding the polypeptide of the present invention.
  • the term “specifically hybridize” as used herein, means that cross-hybridization does not occur significantly with DNA encoding other proteins, under the usual hybridizing conditions, preferably under stringent hybridizing conditions.
  • Such polynucleotides include, probes, primers, nucleotides, and nucleotide derivatives (for example, antisense oligonucleotides, and ribozymes), which specifically hybridize with DNA encoding the polypeptide of the invention or its complementary strand.
  • nucleotide derivatives for example, antisense oligonucleotides, and ribozymes
  • such polynucleotide can be utilized for the preparation of DNA chip.
  • the present invention includes an antisense oligonucleotide that hybridizes with any site within the nucleotide sequence of SEQ ID NO: 1, 3, 5, or 7.
  • This antisense oligonucleotide is preferably against at least 15 continuous nucleotides of the nucleotide sequence of SEQ ID NO: 1, 3, 5, or 7.
  • the above-mentioned antisense oligonucleotide which contains an initiation codon in the above-mentioned at least 15 continuous nucleotides, is even more preferred.
  • antisense oligonucleotides include those comprising the nucleotide sequence of SEQ-ID NO: 16 for suppressing the expression of WDRPUH; SEQ ID NO: 37 for KRZFPUH; SEQ ID NO: 44 for PPIL1; and SEQ ID NO: 89 for APCDD1.
  • Derivatives or modified products of antisense oligonucleotides can be used as antisense oligonucleotides.
  • modified products include lower alkyl phosphonate modifications such as methyl-phosphonate-type or ethyl-phosphonate-type, phosphorothioate modifications and phosphoroamidate modifications.
  • antisense oligonucleotides means, not only those in which the nucleotides corresponding to those constituting a specified region of a DNA or mRNA are entirely complementary, but also those having a mismatch of one or more nucleotides, as long as the DNA or mRNA and the antisense oligonucleotide can specifically hybridize with the nucleotide sequence of SEQ ID NO: 1, 3, 5, or 7.
  • Such polynucleotides are contained as those having, in the “at least 15 continuous nucleotide sequence region”, a homology of at least 70% or higher, preferably at 80% or higher, more preferably 90% or higher, even more preferably 95% or higher.
  • the algorithm stated herein can be used to determine the homology.
  • Such polynucleotides are useful as probes for the isolation or detection of DNA encoding the polypeptide of the invention as stated in a later example or as a primer used for amplifications.
  • the antisense oligonucleotide derivatives of the present invention act upon cells producing the polypeptide of the invention by binding to the DNA or mRNA encoding the polypeptide, inhibiting its transcription or translation, promoting the degradation of the mRNA, and inhibiting the expression of the polypeptide of the invention, thereby resulting in the inhibition of the polypeptide's function.
  • An antisense oligonucleotide derivative of the present invention can be made into an external preparation, such as a liniment or a poultice, by mixing with a suitable base material which is inactive against the derivatives.
  • the derivatives can be formulated into tablets, powders, granules, capsules, liposome capsules, injections, solutions, nose-drops, and freeze-drying agents by adding excipients, isotonic agents, solubilizers, stabilizers, preservatives, pain-killers, and such. These can be prepared by following usual methods.
  • the antisense oligonucleotide derivative is given to the patient by directly applying onto the ailing site or by injecting into a blood vessel so that it will reach the site of ailment.
  • An antisense-mounting medium can also be used to increase durability and membrane-permeability. Examples are, liposome, poly-L-lysine, lipid, cholesterol, lipofectin, or derivatives of these.
  • the dosage of the antisense oligonucleotide derivative of the present invention can be adjusted suitably according to the patient's condition and used in desired amounts. For example, a dose range of 0.1 to 100 mg/kg, preferably 0.1 to 50 mg/kg can be administered.
  • the present invention also includes an siRNA a combination of a sense strand nucleic acid and an antisense strand nucleic acid of the nucleotide sequence of SEQ ID NO: 1, 3, 5, or 7.
  • siRNA is meant a double stranded RNA molecule which prevents translation of a target mRNA. Standard techniques of introducing siRNA into the cell are used, including those in which DNA is a template from which RNA is transcribed.
  • the siRNA comprises a sense nucleic acid sequence and an anti-sense nucleic acid sequence of the polynucleotide encoding human WDRPUH, KRZFPUH, PPIL1L or APCDD1 protein (SEQ ID NO: 1, 3, 5, or 7).
  • the siRNA is constructed such that a single transcript has both the sense and complementary antisense sequences from the target gene, e.g., a hairpin.
  • the method is used to alter gene expression in a cell in which expression of WDRPUH, KRZFPUH, PPIL1, or APCDD1 are up-regulated, e.g., as a result of malignant transformation of the cells. Binding of the siRNA to WDRPUH, KRZFPUH, PPIL1, or APCDD1 transcript in the target cell results in a reduction in the protein production by the cell.
  • the length of the oligonucleotide is at least 10 nucleotides and may be as long as the naturally-occurring transcript. Preferably, the oligonucleotide is 19-25 nucleotides in length.
  • the oligonucleotide is less than 75, 50, or 25 nucleotides in length.
  • WDRPUH KRZFPUH, PPIL1, or APCDD1 siRNA oligonucleotides which inhibit the expression in mammalian cells include oligonucleotides containing any of SEQ ID NO: 93-103. These sequences are target sequence of the following siRNA sequences respectively.
  • the nucleotide sequence of the siRNAs were designed using an siRNA design computer program available from the Ambion website (http://www.ambion.com/techli b/misc/siRNA_finder.html).
  • the computer program selects nucleotide sequences for siRNA synthesis based on the following protocol.
  • the antisense oligonucleotide or siRNA of the invention inhibit the expression of the polypeptide of the invention and is thereby useful for suppressing the biological activity of the polypeptide of the invention.
  • expression-inhibitors comprising the antisense oligonucleotide or siRNA of the invention, are useful in the point that they can inhibit the biological activity of the polypeptide of the invention. Therefore, a composition comprising the antisense oligonucleotide or siRNA of the present invention is useful in treating a cell proliferative disease such as cancer.
  • the present invention provides a method for diagnosing a cell proliferative disease using the expression level of the polypeptides of the present invention as a diagnostic marker.
  • This diagnosing method comprises the steps of: (a) detecting the expression level of the WDRPUH, KRZFPUH, PPIL1, or APCDD1 gene of the present invention; and (b) relating an elevation of the expression level to the cell proliferative disease, such as cancer.
  • the expression levels of the WDRPUH, KRZFPUH, PPIL1, or APCDD1 gene in a particular specimen can be estimated by quantifying mRNA corresponding to or protein encoded by the WDRPUH, KRZFPUH, PPIL1, or APCDD1 gene. Quantification methods for mRNA are known to those skilled in the art. For example, the levels of mRNAs corresponding to the WDRPUH, KRZFPUH, PPIL1, or APCDD1 gene can be estimated by Northern blotting or RT-PCR.
  • nucleotide sequences of the WDRPUH, KRZFPUH, PPIL1, and APCDD1 genes are shown in SEQ ID NO:1, 3, 5, or 7, anyone skilled in the art can design the nucleotide sequences for probes or primers to quantify the WDRPUH, KRZFPUH. PPIL1, or APCDD1 gene.
  • the expression level of the WDRPUH, KRZFPUH, PPIL1, or APCDD1 gene can be analyzed based on the activity or quantity of protein encoded by the gene.
  • a method for determining the quantity of the WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein is shown below.
  • immunoassay method is useful for the determination of proteins in biological materials. Any biological material can be used for the determination of the protein or it's activity. For example, blood sample is analyzed for estimation of the protein encoded by a serum marker.
  • a suitable method can be selected for the determination of the activity of a protein encoded by the WDRPUH, KRZFPUH, PPIL1, or APCDD1 gene according to the activity of each protein to be analyzed.
  • Expression levels of the WDRPUH, KRZFPUH, PPIL1, or APCDD1 gene in a specimen are estimated and compared with those in a normal sample. When such a comparison shows that the expression level of the target gene is higher than those in the normal sample, the subject is judged to be affected with a cell proliferative disease.
  • the expression level of the WDRPUH, KRZFPUH, PPIL1, or APCDD1 gene in the specimens from the normal sample and subject may be determined at the same time. Alternatively, normal ranges of the expression levels can be determined by a statistical method based on the results obtained by analyzing the expression level of the gene in specimens previously collected from a control group.
  • the cell proliferative disease to be diagnosed is preferably cancer. More preferably, when the expression level of the WDRPUH or KRZFPUH gene is estimated and compared with those in a normal sample, the cell proliferative disease to be diagnosed is hepatocellular carcinoma; and when the PPIL1 or APCDD1 gene is estimated for its expression level, then the disease to be diagnosed is colorectal cancer. Further, when the expression level of the KRZFPUH gene is estimated and compared with those in a normal sample, the cell proliferative disease to be diagnosed may be gastric or lung cancer, in addition to hepatocellular carcinoma.
  • a diagnostic agent for diagnosing cell proliferative disease such as cancer including hepatocellular carcinoma and colorectal cancer
  • the diagnostic agent of the present invention comprises a compound that binds to a polynucleotide or a polypeptide of the present invention.
  • an oligonucleotide that hybridizes to the polynucleotide of the present invention, or an antibody that binds to the polypeptide of the present invention may be used as such a compound.
  • the present invention provides a method of screening for a compound for treating a cell proliferative disease using a polypeptide of the present invention.
  • An embodiment of this screening method comprises the steps of: (a) contacting a test compound with a polypeptide of the present invention, (b) detecting the binding activity between the polypeptide of the present invention and the test compound, and (c) selecting a compound that binds to the polypeptide of the present invention.
  • the polypeptide of the present invention to be used for screening may be a recombinant polypeptide or a protein derived from the nature, or a partial peptide thereof.
  • Any test compound for example, cell extracts, cell culture supernatant, products of fermenting microorganism, extracts from marine organism, plant extracts, purified or crude proteins, peptides, non-peptide compounds, synthetic micromolecular compounds, and natural compounds, can be used.
  • the polypeptide of the present invention to be contacted with a test compound can be, for example, a purified polypeptide, a soluble protein, a form bound to a carrier, or a fusion protein fused with other polypeptides.
  • a method of screening for proteins for example, that bind to the polypeptide of the present invention using the polypeptide of the present invention
  • many methods well known by a person skilled in the art can be used.
  • Such a screening can be conducted by, for example, immunoprecipitation method, specifically, in the following manner.
  • the gene encoding the polypeptide of the present invention is expressed in animal cells and so on by inserting the gene to an expression vector for foreign genes, such as pSV2neo, pcDNA I, and pCD8.
  • the promoter to be used for the expression may be any promoter that can be used commonly and include, for example, the SV40 early promoter (Rigby in Williamson (ed.), Genetic Engineering, vol. 3.
  • the EF-1 ⁇ promoter (Kim et al., Gene 91: 217-223(1990)), the CAG promoter (Niwa et al., Gene 108: 193-200 (1991)), the RSV LTR promoter (Cullen, Methods in Enzymology 152: 684-704 (1987)), the SR ⁇ promoter (Takebe et al., Mol Cell Biol 8: 466 (1988)), the CMV immediate early promoter (Seed and Aruffo, Proc Natl Acad Sci USA 84:3365-3369 (1987)), the SV40 late promoter (Gheysen and Fiers, J Mol Appl Genet 1: 385-394(1982)), the Adenovirus late promoter (Kaufman et al., Mol Cell Biol 9: 946(1989)), the HSV TK promoter, and so on.
  • the introduction of the gene into animal cells to express a foreign gene can be performed according to any methods, for example, the electroporation method (Chu et al., Nucleic Acids Res 15: 1311-1326 (1987)), the calcium phosphate method (Chen and Okayama, Mol Cell Biol 7: 2745-2752 (1987)), the DEAE dextran method (Lopata et al., Nucleic Acids Res 12:5707-5717 (1984); Sussman and Milman, Mol Cell Biol 4: 642-1643 (1985)), the Lipofectin method (Derijard, B Cell 7: 1025-1037 (1994); Lamb et al., Nature Genetics 5:22-30 (1993): Rabindran et al., Science 259: 230-234 (1993)), and so on.
  • electroporation method Chou et al., Nucleic Acids Res 15: 1311-1326 (1987)
  • the calcium phosphate method Choen and Okayama, Mol Cell Bio
  • the polypeptide of the present invention can be expressed, as a fusion protein comprising a recognition site (epitope) of a monoclonal antibody by introducing the epitope of the monoclonal antibody, whose specificity has been revealed, to the N- or C-terminus of the polypeptide of the present invention.
  • a commercially available epitope-antibody system can be used (Experimental Medicine 13: 85-90 (1995)).
  • Vectors which can express a fusion protein with, for example, ⁇ -galactosidase, maltose binding protein, glutathione S-transferase, green florescence protein (GFP), and so on by the use of its multiple cloning sites are commercially available.
  • a fusion protein prepared by introducing only small epitopes consisting of several to a dozen amino acids so as not to change the property of the polypeptide of the present invention by the fusion is also reported.
  • Epitopes such as polyhistidine (His-tag), influenza aggregate HA, human c-myc, FLAG, Vesicular stomatitis virus glycoprotein (VSV-GP), T7 gene 10 protein (T7-tag), human simple herpes virus glycoprotein (HSV-tag), E-tag (an epitope on monoclonal phage), and such, and monoclonal antibodies recognizing them can be used as the epitope-antibody system for screening proteins binding to the polypeptide of the present invention (Experimental Medicine 13:85-90(1995)).
  • an immune complex is formed by adding these antibodies to cell lysate prepared using an appropriate detergent.
  • the immune complex consists of the polypeptide of the present invention, a polypeptide comprising the binding ability with the polypeptide, and an antibody.
  • Immunoprecipitation can be also conducted using antibodies against the polypeptide of the present invention, besides using antibodies against the above epitopes, which antibodies can be prepared as described above.
  • an immune complex can be precipitated, for example by Protein A sepharose or Protein G sepharose when the antibody is a mouse IgG antibody.
  • an immune complex can be formed in the same manner as in the use of the antibody against the polypeptide of the present invention, using a substance specifically binding to these epitopes, such as glutathione-Sepharose 4B.
  • Immunoprecipitation can be performed by following or according to, for example, the methods in the literature (Harlow and Lane, Antibodies, 511-552, Cold Spring Harbor Laboratory publications, New York (1988)).
  • SDS-PAGE is commonly used for analysis of immunoprecipitated proteins and the bound protein can be analyzed by the molecular weight of the protein using gels with an appropriate concentration. Since the protein bound to the polypeptide of the present invention is difficult to detect by a common staining method, such as Coomassie staining or silver staining, the detection sensitivity for the protein can be improved by culturing cells in culture medium containing radioactive isotope, 35 S-methionine or 35 S-cystein, labeling proteins in the cells, and detecting the proteins. The target protein can be purified directly from the SDS-polyacrylamide gel and its sequence can be determined, when the molecular weight of a protein has been revealed.
  • a common staining method such as Coomassie staining or silver staining
  • a protein binding to the polypeptide of the present invention can be obtained by preparing a cDNA library from cells, tissues, organs (for example, tissues such as testis for screening proteins binding to WDRPUH; testis, and placenta for screening proteins binding to KRZFPUH; heart, skeletal muscle, testis, thyroid, and adrenal gland for screening those binding to PPIL1; and heart, pancreas, prostate, ovary, lung, liver, kidney, spleen, thymus, colon, and peripheral leukocyte for those binding to APCDD1), or cultured cells expected to express a protein binding to the polypeptide of the present invention using a phage vector (e.g., ZAP), expressing the protein on LB-agarose, fixing the protein expressed on
  • the polypeptide of the invention may be labeled by utilizing the binding between biotin and avidin, or by utilizing an antibody that specifically binds to the polypeptide of the present invention, or a peptide or polypeptide (for example, GST) that is fused to the polypeptide of the present invention. Methods using radioisotope or fluorescence and such may be also used.
  • a two-hybrid system utilizing cells may be used (“MATCHMAKER Two-Hybrid system”, “Mammalian MATCHMAKER Two-Hybrid Assay Kit”, “MATCHMAKER one-Hybrid system” (Clontech); “HybriZAP Two-Hybrid Vector System”(Stratagene); the references “Dalton and Treisman, Cell 68: 597-612 (1992), “Fields and Sternglanz, Trends Genet 10: 286-292 (1994)”).
  • the polypeptide of the invention is fused to the SRF-binding region or GAL4-binding region and expressed in yeast cells.
  • a cDNA library is prepared from cells expected to express a protein binding to the polypeptide of the invention, such that the library, when expressed, is fused to the VP16 or GAL4 transcriptional activation region.
  • the cDNA library is then introduced into the above yeast cells and the cDNA derived from the library is isolated from the positive clones detected (when a protein binding to the polypeptide of the invention is expressed in yeast cells, the binding of the two activates a reporter gene, making positive clones detectable).
  • a protein encoded by the cDNA can be prepared by introducing the cDNA isolated above to E. coli and expressing the protein.
  • Ade2 gene As a reporter gene, for example; Ade2 gene, lacZ gene, CAT gene, luciferase gene, and such can be used in addition to the HIS3 gene.
  • a compound binding to the polypeptide of the present invention can also be screened using affinity chromatography.
  • the polypeptide of the invention may be immobilized on a carrier of an affinity column, and a test compound, containing a protein capable of binding to the polypeptide of the invention, is applied to the column.
  • a test compound herein may be, for example, cell extracts, cell lysates, etc. After loading the test compound, the column is washed, and compounds bound to the polypeptide of the invention can be prepared.
  • test compound When the test compound is a protein, the amino acid sequence of the obtained protein is analyzed, an oligo DNA is synthesized based on the sequence, and cDNA libraries are screened using the oligo DNA as a probe to obtain a DNA encoding the protein.
  • a biosensor using the surface plasmon resonance phenomenon may be used as a mean for detecting or quantifying the bound compound in the present invention.
  • the interaction between the polypeptide of the invention and a test compound can be observed real-time as a surface plasmon resonance signal, using only a minute amount of polypeptide and without labeling (for example, BIAcore, Pharmacia). Therefore, it is possible to evaluate the binding between the polypeptide of the invention and a test compound using a biosensor such as BIAcore.
  • a compound isolated by the screening is a candidate for drugs which promote or inhibit the activity of the polypeptide of the present invention, for treating or preventing diseases attributed to, for example, cell proliferative diseases, such as cancer.
  • a compound in which a part of the structure of the compound obtained by the present screening method having the activity of binding to the polypeptide of the present invention is converted by addition, deletion and/or replacement, is included in the compounds obtained by the screening method of the present invention.
  • the present invention provides methods for screening candidate agents which are potential targets in the treatment of cell proliferative disease.
  • candidate agents which are potential targets in the treatment of cell proliferative disease, can be identified through screenings that use the expression levels and activities of WDRPUH, KRZFPUH, PPIL1, or APCDD1 as indices.
  • such screening may comprise, for example, the following steps:
  • Cells expressing at least one of the WDRPUH, KRZFPUH, PPIL1, or APCDD1 include, for example, cell lines established from HCC or colorectal carcinomas; such cells can be used for the above screening of the present invention.
  • the expression level can be estimated by a methods well known by one skilled in the art. In the method of screening, a compound that reduces the expression level of at least one of WDRPUH, KRZFPUH, PPIL1, or APCDD1 can be selected as candidate agents.
  • the method utilizes the biological activity of the polypeptide of the present invention as an index. Since the WDRPUH, KRZFPUH, PPIL1, and APCDD1 proteins of the present invention have the activity of promoting cell proliferation, a compound which promotes or inhibits this activity of one of these proteins of the present invention can be screened using this activity as an index.
  • This screening method includes the steps of: (a) contacting a test compound with the polypeptide of the present invention; (b) detecting the biological activity of the polypeptide of step (a); and (c) selecting a compound that suppresses the biological activity of the polypeptide in comparison with the biological activity detected in the absence of the test compound.
  • Any polypeptides can be used for screening so long as they comprise the biological activity of the WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein.
  • biological activity include cell-proliferating activity of the human WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein, the activity of PPIL1 to bind to SNW1 or stathmin.
  • a human WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein can be used and polypeptides functionally equivalent to these proteins can also be used.
  • Such polypeptides may be expressed endogenously or exogenously by cells.
  • test compounds for example, cell extracts, cell culture supernatant, products of fermenting microorganism, extracts of marine organism, plant extracts, purified or crude proteins, peptides, non-peptide compounds, synthetic micromolecular compounds, or natural compounds, can be used.
  • the compound isolated by this screening is a candidate for agonists or antagonists of the polypeptide of the present invention.
  • agonist refers to molecules that activate the function of the polypeptide of the present invention by binding to the polypeptide.
  • antagonist refers to molecules that inhibit the function of the polypeptide of the present invention by binding to the polypeptide.
  • a compound isolated by this screening is a candidate for compounds which inhibit the in vivo interaction of the polypeptide of the present invention with molecules (including DNAs and proteins).
  • the biological activity to be detected in the present method is cell proliferation
  • it can be detected, for example, by preparing cells which express the polypeptide of the present invention, culturing the cells in the presence of a test compound, and determining the speed of cell proliferation, measuring the cell cycle and such, as well as by measuring the colony forming activity as described in the Examples.
  • the compound isolated by the above screenings is a candidate for drugs which inhibit the activity of the polypeptide of the present invention and can be applied to the treatment of diseases associated with the polypeptide of the present invention, for example, cell proliferative diseases including cancer. More particularly, when the biological activity of WDRPUH or KRZFPUH protein is used as the index, compounds screened by the present method serve as a candidate for drugs for the treatment of hepatocellular carcinoma. Furthermore, when the biological activity of KRZFPUH protein is used as the index, apart from HCC, compounds screened by the present method serve as a candidate for drugs for the treatment of gastric or lung carcinoma. On the other hand, when the biological activity of PPIL1 or APCDD1 protein is used as the index, compounds screened by the present method serve as a candidate for drugs for the treatment of colorectal carcinoma.
  • compound in which a part of the structure of the compound inhibiting the activity of WDRPUH, KRZFPUH, PPIL1, or APCDD1 proteins is converted by addition, deletion and/or replacement are also included in the compounds obtainable by the screening method of the present invention.
  • the screening method of the present invention may comprise the following steps:
  • Suitable reporter genes and host cells are well known in the art.
  • the reporter construct required for the screening can be prepared by using the transcriptional regulatory region of a marker gene.
  • a reporter construct can be prepared by using the previous sequence information.
  • a nucleotide segment containing the transcriptional regulatory region can be isolated from a genome library based on the nucleotide sequence information of the marker gene.
  • the method utilizes the promoter region of APCDD1.
  • the ⁇ -catenin/Tcf4 complex was discovered to bind to the two Tcf/LEF binding motifs in the transcriptional regulatory region of the APCDD1 gene and to be involved in the transcriptional activation of APCDD1. Therefore, compounds that inhibit the activation of the transcription of APCDD1 serve as candidates for drugs which inhibit the activity of the APCDD1 polypeptide of the present invention and can be applied to the treatment of diseases associated with the polypeptide, for example, cell proliferative diseases, such as cancer, especially colorectal cancer.
  • This screening method includes the steps of: (a) constructing a vector comprising the two Tcf/LEF binding motifs of APCDD1 upstream of a reporter gene; transforming a cell with the vector of step (a); (c) contacting a test compound and the ⁇ -catenin/Tcf-4 complex with the cell of step (b); (d) detecting the expression of the reporter gene; and (e) selecting a compound that suppresses the expression of the reporter gene in comparison to that in the absence of the test compound.
  • test compound for example, cell extracts, cell culture supernatant, products of fermenting microorganism, extracts from mare organism, plant extracts, purified or crude proteins, peptides, non-peptide compounds, synthetic micromolecular compounds, and natural compounds, can be used.
  • the screening can be conducted, for example, according to the method described in Example 28.
  • the vector comprising the two Tcf/LEF binding motifs of APCDD1 upstream of a reporter gene can be constructed by inserting the promoter region of APCDD1 into an expression vector comprising the reporter gene.
  • the promoter region of APCDD1 may be obtained from genomic libraries using the 5′ region of the human APCDD1 gene (SEQ ID NO: 7) as the probe.
  • ⁇ -catenin and Tcf4 can be prepared as in Example 28.
  • reporter gene Any reporter gene may be used in the screening so long as its expression can be detected.
  • reporter genes include ⁇ -gal gene, the CAT gene, and the luciferase gene. Detection of the expression of the reporter gene can be conducted corresponding to the type of the reporter gene.
  • preferable examples include HeLa cells.
  • the compound isolated by the screening is a candidate for drugs which inhibit the expression of the APCDD1 protein of the present invention and can be applied to the treatment of diseases associated with the APCDD1 protein, for example, cell proliferative diseases such as cancer, more particularly colorectal carcinoma.
  • diseases associated with the APCDD1 protein for example, cell proliferative diseases such as cancer, more particularly colorectal carcinoma.
  • compounds in which a part of the structure of the compound inhibiting the transcriptional activation of the APCDD1 protein by the ⁇ -catenin/Tcf-4 complex is converted by addition, deletion, substitution and/or insertion are also included in the compounds obtainable by the screening method of the present invention.
  • the method utilizes the binding ability of PPIL1 to SNW1 (SKI interacting protein) or stathmin.
  • SNW1 SKI interacting protein
  • stathmin a cytosolic phosphorprotein involved in the progression of the cell cycle.
  • the inhibition of the binding between the PPIL1 protein and SNW1 or stathmin leads to the suppression of cell proliferation
  • compounds inhibiting the binding serve as pharmaceuticals for treating cell proliferative disease such as cancer.
  • the cell proliferative disease treated by the compound screened by the present method is colorectal cancer.
  • This screening method includes the steps of (a) contacting a polypeptide of the present invention with stathmin or SNW1 in the presence of a test compound; (b) detecting the binding between the polypeptide and stathmin or SNW1; and (c) selecting the compound that inhibits the binding between the polypeptide and stathmin or SNW1.
  • the PPIL1 polypeptide of the present invention, and SNW1 or stathmin to be used for the screening may be a recombinant polypeptide or a protein derived from the nature, or may also be a partial peptide thereof so long as it retains the binding ability to each other.
  • the PPIL1 polypeptide, SNW1 or stathmin to be used in the screening can be, for example, a purified polypeptide, a soluble protein, a form bound to a carrier, or a fusion protein fused with other polypeptides.
  • test compound for example, cell extracts, cell culture supernatant, products of fermenting microorganism, extracts from marine organism, plant extracts, purified or crude proteins, peptides, non-peptide compounds, synthetic micromolecular compounds, and natural compounds, can be used.
  • a method of screening for compounds that inhibit the binding between the PPIL1 protein and SNW1 or stathmin many methods well known by one skilled in the art can be used. Such a screening can be carried out as an in vitro assay system, for example, in a cellular system. More specifically, first, either the PPIL1 polypeptide, or SNW1 or stathmin is bound to a support, and the other protein is added together with a test sample thereto. Next, the mixture is incubated, washed, and the other protein bound to the support is detected and/or measured.
  • supports that may be used for binding proteins include insoluble polysaccharides, such as agarose, cellulose, and dextran; and synthetic resins, such as polyacrylamide, polystyrene, and silicon; preferably commercial available beads, and plates (e.g., multi-well plates, biosensor chip, etc.) prepared from the above materials may be used. When using beads, they may be filled into a column.
  • insoluble polysaccharides such as agarose, cellulose, and dextran
  • synthetic resins such as polyacrylamide, polystyrene, and silicon
  • beads e.g., multi-well plates, biosensor chip, etc.
  • binding of a protein to a support may be conducted according to routine methods, such as chemical bonding, and physical adsorption.
  • a protein may be bound to a support via antibodies specifically recognizing the protein.
  • binding of a protein to a support can be also conducted by means of avidin and biotin binding.
  • the binding between proteins is carried out in buffer, for example, but are not limited to, phosphate buffer and Tris buffer, as long as the buffer does not inhibit the binding between the proteins.
  • a biosensor using the surface plasmon resonance phenomenon may be used as a mean for detecting or quantifying the bound protein.
  • the interaction between the proteins can be observed real-time as a surface plasmon resonance signal, using only a minute amount of polypeptide and without labeling (for example, BIAcore, Pharmacia). Therefore, it is possible to evaluate the binding between the PPIL1 polypeptide and SNW1 or stathmin using a biosensor such as BIAcore.
  • either the PPIL1 polypeptide, or SNW1 or stathmin may be labeled, and the label of the bound protein may be used to detect or measure the bound protein. Specifically, after pre-labeling one of the proteins, the labeled protein is contacted with the other protein in the presence of a test compound, and then, bound proteins are detected or measured according to the label after washing.
  • Labeling substances such as radioisotope (e.g., 3 H, 14 C, 32 P, 35 S, 125 I, 131 I), enzymes (e.g. alkaline phosphatase, horseradish peroxidase, ⁇ -galactosidase, ⁇ -glucosidase), fluorescent substances (e.g., fluorescein isothiosyanete (FITC), rhodamine), and biotin/avidin, may be used for the labeling of a protein in the present method.
  • radioisotope e.g., 3 H, 14 C, 32 P, 35 S, 125 I, 131 I
  • enzymes e.g. alkaline phosphatase, horseradish peroxidase, ⁇ -galactosidase, ⁇ -glucosidase
  • fluorescent substances e.g., fluorescein isothiosyanete (FITC), rhodamine
  • proteins labeled with enzymes can be detected or measured by adding a substrate of the enzyme to detect the enzymatic change of the substrate, such as generation of color, with absorptiometer.
  • the bound protein may be detected or measured using fluorophotometer.
  • the binding of the PPIL1 polypeptide and SNW1 or stathmin can be also detected, or measured using antibodies to the PPIL1 polypeptide and SNW1 or stathmin.
  • the mixture is incubated and washed, and detection or measurement can be conducted using an antibody against SNW1 or stathmin.
  • SNW1 or stathmin may be immobilized on a support, and an antibody against PPIL1 may be used as the antibody.
  • the antibody is preferably labeled with one of the labeling substances mentioned above, and detected or measured based on the labeling substance.
  • the antibody against the PPIL1 polypeptide, SNW1, or stathmin may be used as a primary antibody to be detected with a secondary antibody that is labeled with a labeling substance.
  • the antibody bound to the protein in the screening of the present invention may be detected or measured using protein G or protein A column.
  • a two-hybrid system utilizing cells may be used (MATCHMAKER Two-Hybrid system”, “Mammalian MATCHMAKER Two-Hybrid Assay Kit”, “MATCHMAKER one-Hybrid system” (Clontech); “HybriZAP Two-Hybrid Vector System” (Stratagene); the references “Dalton and Treisman, Cell 68: 597-612 (1992)”, “Fields and Sternglanz, Trends Genet 10: 286-92 (1994)”).
  • the PPIL1 polypeptide of the invention is fused to the SRF-binding region or GAL4-binding region and expressed in yeast cells.
  • the SNW1 or stathmin binding to the PPIL1 polypeptide of the invention is fused to the VP16 or GAL4 transcriptional activation region and also expressed in the yeast cells in the existence of a test compound.
  • the test compound does not inhibit the binding between the PPIL1 polypeptide and SNW1 or stathmin, the binding of the two activates a reporter gene, making positive clones detectable.
  • reporter gene for example, Ade2 gene, lacZ gene, CAT gene, luciferase gene and such can be used besides HIS3 gene.
  • the compound isolated by the screening is a candidate for drugs which inhibit the activity of the PPIL1 protein of the present invention and can be applied to the treatment of diseases associated with the PPIL1 protein, for example, cell proliferative diseases such as cancer, more particularly colorectal carcinoma.
  • diseases associated with the PPIL1 protein for example, cell proliferative diseases such as cancer, more particularly colorectal carcinoma.
  • compounds in which a part of the structure of the compound inhibiting the binding between the PPIL1 protein and SNW1 or stathmin is converted by addition, deletion, substitution and/or insertion are also included in the compounds obtainable by the screening method of the present invention.
  • the isolated compound When administrating the compound isolated by the methods of the invention as a pharmaceutical for humans and other mammals, such as mice, rats, guinea-pigs, rabbits, chicken, cats, dogs, sheep, pigs, cattle, monkeys, baboons, chimpanzees, for treating a cell proliferative disease (e.g., cancer) the isolated compound can be directly administered or can be formulated into a dosage form using known pharmaceutical preparation methods.
  • the drugs can be taken orally, as sugarcoated tablets, capsules, elixirs, and microcapsules, or non-orally, in the form of injections of sterile solutions or suspensions with water or any other pharmaceutically acceptable liquid.
  • the compounds can be mixed with pharmacologically acceptable carriers or medium, specifically, sterilized water, physiological saline, plant-oil, emulsifiers, suspending agents, surfactants, stabilizers, flavoring agents, excipients, vehicles, preservatives, binders, and such, in a unit dose form, required for generally accepted drug implementation.
  • pharmacologically acceptable carriers or medium specifically, sterilized water, physiological saline, plant-oil, emulsifiers, suspending agents, surfactants, stabilizers, flavoring agents, excipients, vehicles, preservatives, binders, and such, in a unit dose form, required for generally accepted drug implementation.
  • the amount of active ingredients in these preparations makes a suitable dosage within the indicated range acquirable.
  • additives that can be mixed to tablets and capsules are, binders such as gelatin, corn starch, tragacanth gum, and arabic gum; excipients such as crystalline cellulose; swelling agents such as corn starch, gelatin and alginic acid; lubricants such as magnesium stearate; sweeteners such as sucrose, lactose or saccharin; flavoring agents such as peppermint, Gaultheria adenothrix oil, and cherry.
  • a liquid carrier such as oil, can also be further included in the above ingredients.
  • Sterile composites for injections can be formulated following normal drug implementations using vehicles such as distilled water used for injections.
  • Physiological saline, glucose and other isotonic liquids including adjuvants, such as D-sorbitol, D-mannnose, D-mannitol, and sodium chloride can be used as aqueous solutions for injections.
  • adjuvants such as D-sorbitol, D-mannnose, D-mannitol, and sodium chloride
  • solubilizers such as alcohol, specifically ethanol, polyalcohols such as propylene glycol and polyethylene glycol, non-ionic surfactants, such as Polysorbate 80 (TM) and HCO-50.
  • Sesame oil or Soy-bean oil can be used as a oleaginous liquid and may be used in conjunction with benzyl benzoate or benzyl as a solubilizers and may be formulated with a buffer, such as phosphate buffer and sodium acetate buffer; a pain-killer, such as procaine hydrochloride; a stabilizer, such as benzyl alcohol, phenol; and an anti-oxidant.
  • the prepared injection may be filled into a suitable ampule.
  • Methods well known to one skilled in the art may be used to administer the inventive pharmaceutical compound to patients, for example as intraarterial, intravenous, percutaneous injections and also as intranasal, transbronchial, intramuscular, or oral administrations.
  • the dosage and method of administration vary according to the body-weight and age of a patient and the administration method; however, one skilled in the art can routinely select them. If said compound is encodable by a DNA, the DNA can be inserted into a vector for gene therapy and the vector administered to perform the therapy.
  • the dosage and method of administration vary according to the body-weight, age, and symptoms of a patient but one skilled in the art can select them suitably.
  • the dose of a compound that binds with the polypeptide of the present invention and regulates its activity is about 0.1 mg to about 100 mg per day, preferably about 1.0 mg to about 50 mg per, day and more preferably about 1.0 mg to about 20 mg per day, when administered orally to a normal adult (weight 60 kg).
  • the present invention provides a method for treating or preventing a cell proliferative disease, such as cancer, using an antibody against the polypeptide of the present invention.
  • a pharmaceutically effective amount of an antibody against the polypeptide of the present invention is administered. Since the expression of the WDRPUH, KRZFPUH, PPIL1, and APCDD1 protein are up-regulated in cancer cells, and the suppression of the expression of these proteins leads to the decrease in cell proliferating activity, it is expected that cell proliferative diseases can be treated or prevented by binding the antibody and these proteins.
  • an antibody against the polypeptide of the present invention are administered at a dosage sufficient to reduce the activity of the protein of the present invention, which is in the range of 0.1 to about 250 mg/kg per day.
  • the dose range for adult humans is generally from about 5 mg to about 17.5 g/day, preferably about 5 mg to about 10 g/day, and most preferably about 100 mg to about 3 g/day.
  • an antibody binding to cell surface marker specific for tumor cell can be used as a tool for drug delivery.
  • the antibody having a cytotoxic agent are administered at a dosage sufficient to injure the tumor cell.
  • the present invention also relates to a method of inducing anti-tumor immunity comprising a step of administering WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein or an immunologically active fragment thereof, or nucleic acids encoding any one of the protein and the fragments thereof.
  • WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein or the immunologically active fragments thereof are useful as vaccines against cell proliferative disease.
  • vaccine against cell proliferative disease refers to a substance that has the effect of inducing anti-tumor immunity when it is inoculated upon animals.
  • anti-tumor immunity includes immune responses such as the following:
  • the protein when inoculation of a certain protein into an animal induces any one of these immune responses, the protein is said to have an anti-tumor immunity inducing effect.
  • the induction of the anti-tumor immunity by a protein can be detected by observing the response of the immune system in the host against the protein ice vivo or in vitro.
  • cytotoxic T lymphocytes For example, a method for detecting the induction of cytotoxic T lymphocytes is well known.
  • a foreign substance that enters the living body is presented to T cells and B cells by the action of antigen presenting cells (APCs).
  • APCs antigen presenting cells
  • T cells that respond to the antigen presented by APC in antigen specific manner differentiate into cytotoxic T cells (or cytotoxic T lymphocytes; CTLs due to the stimulation by the antigen, and then proliferate (this is referred to as activation of T cells). Therefore, CTL induction by a certain peptide can be evaluated by presenting the peptide to T cell by APC, and detecting induction of CTL.
  • APC has the effect of activating CD4+ T cells, CD8+ T cells, macrophages, eosinophils, and NK cells. Since CD4+ T cells and CD8+ T cells are also important in anti-tumor immunity, the anti-tumor immunity inducing action of the peptide can be evaluated using the activation effect of these cells as indicators.
  • DC dendritic cells
  • APC dendritic cells
  • DC is a representative APC having the strongest CTL inducing action.
  • the test polypeptide is initially contacted with DC, and then this DC is contacted with T cells. Detection of T cells having cytotoxic effects against the cells of interest after contacting with DC shows that the test polypeptide has an activity of inducing the cytotoxic T cells.
  • Activity of CTL against tumors can be detected, for example, using the lysis of 51 Cr-labeled tumor cells as the indicator.
  • APC is not limited to DC, and peripheral blood mononuclear cells (PBMCs) may be used.
  • PBMCs peripheral blood mononuclear cells
  • CL has been shown to be induced by culturing PBMC in the presence of keyhole limpet hemocyanin (KLH) and IL-7.
  • test polypeptides confirmed to possess CTL inducing activity by these methods are polypeptides having DC activation effect and subsequent CTL inducing activity. Therefore, polypeptides that induce CTL against tumor cells are useful as vaccines against tumors. Furthermore, APC that acquired the ability to induce CTL against tumors by contacting with the polypeptides are useful as vaccines against tumors. Furthermore, CTL that acquired cytotoxicity due to presentation of the polypeptide antigens by APC can be also used as vaccines against tumors. Such therapeutic methods for tumors using anti-tumor immunity due to APC and CTL are referred to as cellular immunotherapy.
  • induction of anti-tumor immunity by a polypeptide can be confirmed by observing the induction of antibody production against tumors. For example, when antibodies against a polypeptide are induced in a laboratory animal immunized with the polypeptide, and when growth of tumor cells is suppressed by those antibodies, the polypeptide has the ability to induce anti-tumor immunity.
  • Anti-tumor immunity is induced by administering the vaccine of this invention, and this enables treatment and prevention of HCC or colon cancer.
  • Therapy against cancer, or effect of preventing the onset of cancer may be any one of the following steps, such as inhibitory activity against growth of cancerous cells, involution of cancer, and suppression of occurrence of cancer. Otherwise, it may be decrease of mortality of individuals having cancer, decrease of tumor markers in the blood, alleviation of detectable symptoms accompanying cancer, or such.
  • Such effects are preferably statistically significant, for example, observation, at a significance level of 5% or less, of therapeutic effect against cancer, or preventive effect against cancer onset compared to a control to which the vaccine was not administered is preferred.
  • Student's t-test, the Mann-Whitney U-test, or ANOVA may be used for statistical analyses.
  • the above-mentioned protein having immunological activity or a vector encoding the protein may be combined with an adjuvant.
  • An adjuvant refers to a compound that enhances the immune response against the protein when administered together (or successively) with the protein having immunological activity.
  • adjuvants include cholera toxin, salmonella toxin, alum, and such, but are not limited thereto.
  • the vaccine of this invention may be combined appropriately with a pharmaceutically acceptable carrier. Examples of such carriers are sterilized water, physiological saline, phosphate buffer, culture fluid, and such. Furthermore, it may contain as necessary, stabilizers, suspensions, preservatives, surfactants, and such.
  • the vaccine is administered systemically or locally. Vaccine administration may be by single administration, or boosted by multiple administrations.
  • tumors can be treated or prevented, for example, by the ex vivo method. More specifically, PBMCs of the subject receiving treatment or prevention are collected, the cells are contacted with the polypeptide ex vivo, and after inducing APC or CTL, the cells can be administered to the subject.
  • APC can be also induced by introducing a vector encoding the polypeptide into PBMCs ex vivo.
  • APC or CTL induced in vitro can be cloned prior to administration. By cloning and growing cells which have high activity of damaging target cells, cellular immunotherapy can be performed more effectively.
  • APC and CTL isolated in this manner may be used for cellular immunotherapy not only against individuals from whom the cells are derived, but also against similar types of tumors from other individuals.
  • a pharmaceutical composition for treating or, preventing a cell proliferative disease, such as cancer comprising a pharmaceutically effective amount of the polypeptide of the present invention.
  • the pharmaceutical composition may be used for raising anti tumor immunity.
  • the normal expression of WDRPUH and KRZFPUH are restricted to testis, and placenta and testis, respectively, and therefore, suppression of these genes may not adversely affect other organs.
  • the WDRPUH and KRZFPUH polypeptides are preferable for treating cell proliferative disease, especially HCCs.
  • HCC tissues were obtained with informed consent from surgical specimens of patients who underwent surgery.
  • Total RNA was extracted from microdissected tissue with Qiagen RNeasy kit (Qiagen) or Trizol reagent (Life Technologies) according to the manufacturers' protocol.
  • the extracted total RNA was treated with DNase I, amplified with Ampliscribe T7 Transcription Kit (Epicentre Technologies) and labeled during reverse transcription using Cy-dye. (Amersham).
  • Cy5 and Cy3 were used for labeling RNAs from non-cancerous tissue and tumor, respectively. Then, hybridization, washing, and detection were carried out according to the method of Ono et al. (Cancer Res 60: 5007-11(2000)). The fluorescent intensity of Cy5 and Cy3 at each target spot was measured using Array Vision software (Amersham Pharmacia). The measurement was conducted in duplicate, and after subtracting background signal from the detected fluorescent intensities at each target spot, the average was calculated. Then, all fluorescent intensities detected on slides were normalized to adjust the mean Cy5 and Cy3 intensity of 52 housekeeping genes for each slide. Genes with a fluorescent intensity below 25000 units for both Cy3 and Cy5 were excluded from further investigation, and genes with >2.0 Cy3/Cy5 signal ratios were selected for further evaluation.
  • HCCs a gene with in-house accession number D3197, corresponding to an EST (Hs. 122614) of UniGene cluster (http://www.ncbi.nlm.nih.gov/UniGene/), was over-expressed in eleven of twelve HCCs compared with the corresponding no-cancerous liver tissues ( FIG. 1 a ).
  • the gene comprised an open reading frame encoding a protein with WD40 repeats, and thus was dubbed WDRPUH(WD40 repeats protein up-regulated in HCCs). WDRPUH was also up-regulated in 1 of 2 cases of gastric cancer.
  • gene with the in-house accession number C6242 EST Hs.
  • KRZFPUH Krupple-type zinc finger protein up-regulated in HCC
  • the amplification was conducted using GeneAmp PCR system 9700 (Perkin-Elmer) under following condition: denaturing at 94° C. for 4 min; 35 cycles of 94° C. for 30 s, 56° C. for 30 s, and 72° C. for 45 s.
  • multi-tissue northern blot analysis was performed using the PCR product of WDRPUH as a probe. More specifically, human multiple-tissue blots (Clontech) were hybridized with 32 P-labeled PCR product of WDRPUH. Pre-hybridization, hybridization, and washing were performed according to the supplier's recommendations. The blots were autoradiographed with intensifying screens as ⁇ 80° C. for 24 to 72 h. As a result, a 2-kb transcript was detected to be abundantly expressed in testis ( FIG. 2 a ). Since D3197 was smaller than the WDRPUH cDNA detected on the Northern blot, next the inventors investigated the 5′ sequence of WDRPUH cDNA.
  • genomic sequence corresponding to D3197 was searched in genomic databases (http://www.ncbi.nlm.nih.gov/BLAST/) using BLAST program to find a cosmid sequence (GenBank Accession No. AC026855) assigned to chromosomal band 17 p13.
  • Candidate-exon sequences of the genomic sequence were predicted using GENSCAN, Gene Recognition, and Assembly Internet ink program, and the predicted exon sequences were connected.
  • 5′ rapid amplification of cDNA ends (5′-RACE) was carried as follows: 5′ RACE was carried out using Marathon cDNA amplification kit (Clontech) according to the manufacturer's instruction.
  • the 5′ part of WDRPUH was prepared using gene-specific reverse primers 5′-TTACCGTCGTTCCATGCTGAAATGATGC-3′ [SEQ ID NO:13] and AP-1 primer supplied with the kit.
  • cDNA template was synthesized from human testis mRNA (Clontech), and the amplified product was cloned using TA cloning kit (Invitrogen) to determine its sequence with ABI PRISM 3700 DNA sequencer (Applied Biosystems). The determined assembled sequence consisted of 2152 nucleotides containing an open reading frame of 1860 nucleotides encoding a protein of '620 amino acid residues (GenBank Accession No. AB065281).
  • the entire coding region corresponding to WDRPUH was amplified using gene specific primer set: 5′-GGGGTACCACCATGGATAACAAAATTTCGCCGGAG-3′ [SEQ ID NO: 14] and 5′-CGGAATTCTCAGGAGGTATATGGGTACTTCCATGC-3′ [SEQ ID NO: 15]; and cloned into pcDNA3.1myc/His vector (Invitrogen). Then, the constructed vector pcDNA3.1myc/His-WDRPUH was transiently transfected into SNU475 cells (Korea cell-line bank) and the cells were grown in RPMI1640.
  • the cells were fixed with PBS containing 4% paraformaldehyde for 15 min, then permeabilized with PBS containing 0.1% Triton X-100 for 2.5 min at room temperature (RT). Subsequently, cells were covered with 2% BSA in PBS for 24 h at 4° C. to block non-specific hybridization. 1:1000 diluted mouse anti-myc monoclonal antibody (Sigma) was used as the primary oantibody for immunocytochemical staining, and the reaction was visualized after incubation with Rhodamine-conjugated anti-mouse secondary antibody (Leinco and ICN). Nuclei were counter-stained with 4′,6′-diamidine-2′-phenylindole dihydrochloride (DAPI). Fluorescent images were obtained under an ECLIPSE E800 microscope. As a result, the tagged-WDRPUH protein was revealed to be present in the cytoplasm of the cells ( FIG. 3 ).
  • the transfected cells were incubated in Dulbecco's modified Eagle's medium (DMEM) with appropriate concentration of geneticin for 10 to 21 days. Then, the cells were fixed with 100% methanol and stained by Giemsa solution. All experiments were carried out in triplicate.
  • DMEM Dulbecco's modified Eagle's medium
  • SNU475 cells Karl cell-line bank
  • 10-cm dishes (2 ⁇ 10 5 cells/dish) were transfected with antisense S-oligonucleotides encompassing the first exon-intron boundary of WDRPUH (WDRPUH-AS4; 5′-GGCCTCACCATTGAAG-3′ [SEQ ID NO: 16]) or control S-oligonucleotides (WDRPUH-S4; 5′-CTTCAATGGTGAGGCC-3′ [SEQ ID NO: 17]) using LIPOFECTIN Reagent (GIBCO BRL); and cultured in RPMI1640 supplemented with an appropriate concentration of geneticin for six to twelve days.
  • the cells were analyzed for their expression of WDRPUH and GAPDH by RT-PCR and western blo
  • a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay was performed by plating SNU475 cells at a density of 5 ⁇ 10 5 cells/100 mm dish.
  • the cells were transfected in triplicate with sense or antisense S-oligonucleotides designated to suppress WDRPUH.
  • the medium was replaced with fresh medium containing 500 ⁇ g/ml of MTT (Sigma) and the plates were incubated for 4 h at 37° C.
  • the cells were lysed by the addition of 1 ml of 0.01 N HCl/10% SDS.
  • the color reaction was quantified with an ELISA plate reader at a test wavelength of 570 nm (reference 630 nm).
  • the cell viability was represented by the absorbance compared to the control.
  • short interfering RNA composed of 20 to 21-mer double stranded RNA (dsRNA) with 19 complementary nucleotides and 3′ terminal complementary dimers of thymidine or uridine
  • dsRNA double stranded RNA
  • the present inventors constructed plasmids expressing various WDRPUH-siRNAs and examined their effect on WDRPUH expression.
  • psiH1BX3.0 vector was constructed as follows. Since H1RNA gene was reported to be transcribed by RNA polymerase III, which produce short transcripts with uridines at the 3′ end, the genomic fragment of H1RNA gene containing its promoter region was amplified by PCR using a set of primers: 5′-TGGTAGCCAAGTGCAGGTTATA-3′ [SEQ ID NO: 18] and 5′-CCAAAGGGTTTCTGCAGTTTCA-3′ [SEQ ID NO: 19]; and human placental DNA as a template. The product was purified and cloned into pCR2.0 plasmid vector using TA cloning kit (Invitrogen) according to the supplier's protocol.
  • TA cloning kit Invitrogen
  • a fragment containing the H1RNA gene was amplified by PCR with a set of primers: 5′-TGCGGATCCAGAGCAGATTGTACTGAGAGT-3′[SEQ ID NO: 20] and 5′-CTCTATCTCGAGTGAGGCGGAAAGAACCA-3′ [SEQ ID NO: 21]; digested with BamHI and XhoI, and was purified. Then, the purified BamHI-XhoI fragment containing the H1RNA gene was cloned into nucleotide 1257 to 56 fragment of pcDNA3.1(+) (Invitrogen). The ligated DNA was used as a template for PCR with primers:
  • Control plasmid and plasmids expressing WDRPUH-siRNAs were prepared by cloning double-stranded oligonucleotides into the BbsI site of psiH1BX3.0 vector.
  • the oligonucleotides cloned into the vector was as follows:
  • the target sequence of siRNA in each of the sequences is underlined.
  • psiH1BX-WDRPUH01 but not psiH1BX-WDRPUH02, psiH1BX-WDRPUH03 or psiH1BX-WDRPUH05 significantly suppressed expression of WDRPUH in the cells ( FIG. 6A ).
  • HepG2 cells were transfected with psiH1BX-WDRPUH01, psiH1BX-WDRPUH02, psiH1BX-WDRPUH03, or psiH1BX-WDRPUH05, psiH1BX-EGFP or mock vector.
  • Viable cells transfected with psiH1BX-WDRPUH01 were markedly reduced compared to those transfected with psiH1BX-WDRPUH02, psiH1BX-WDRPUH03, or psiH1BX-WDRPUH05, psiH1BX-EGFP or the control, suggesting that decreased expression of WDRPUH suppresses the growth of hepatoma cells ( FIG. 6B ).
  • polyclonal antibody against WDRPUH was prepared as follows. First, recombinant His-tagged WDRPUH was produced in E. coli and purified from the cells using Pro BondTM histidine Resin (Invitrogen) according to the manufacturer's recommendations. The recombinant protein was used for the immunization of rabbits. The polyclonal antibody against WDRPUH was purified from the sera.
  • the immunoblotting with the anti-WDRPUH sera but not pre-immune sera showed a 70 kD band of FLAG-tagged WDRPUH, which was identical by size to that detected using anti-FLAG antibody ( FIG. 7 ).
  • Multi-tissue northern blot analysis was conducted as in Example 2 using C6242 cDNA as a probe. The result showed that a 2.8-kb transcript was abundantly expressed in placenta and testis ( FIG. 8 a ). Since C6242 was smaller than that detected on Northern blot, the sequence of the 5′ part of KRZFPUH cDNA was investigated. First, the genomic sequences corresponding to C6242 was searched using BLAST program in genomic databases (http://www.ncbi.nlm.nih.gov/BLAST/) to find a working draft sequence (GenBank accession number:NT-024802) that had been assigned to chromosomal band 16p11.
  • 5′RACE was carried out as in Example 2 except 5′-TAGATTCTGGGCGCACTTGTGGCTCTCC-3′ [SEQ ID NO: 34] was used as the primer to consequently obtain an, assembled sequence of 2744 nucleotides containing an open reading frame of 1500 nucleotides encoding a 500-amino-acid protein (GenBank Accession No. AB065282).
  • the entire coding region corresponding to KRZFPUH was amplified using gene specific primer set: 5′-GGGGTACCACCATGGCGCCACCTTCG-3′[SEQ ID NO: 35] and 5′-CGGAATTCATGGGCGTTGCCCCTCTGACTGG-3′ [SEQ ID NO: 36]; and cloned into a pcDNA3.1myc/His vector (Invitrogen). Then this construct was transiently transfected into SNU475 cells (Korea cell-line bank) and subcellular localization of KRZFPUH was studied as in Example 3. The immunocytochemical staining of the cells revealed that the tagged-KRZFPUH protein was present in the nucleus ( FIG. 9 ).
  • the transfected cells were incubated in DMEM with appropriate concentration of geneticin for 10 to 21 days. Then, the cells were fixed with 100% methanol and stained by Giemsa solution. AU experiments were carried out in triplicate. Compared with control plasmids expressing complementary strand of KRZFPUH (pcDNA-antisense), pcDNA-KRZFPUH produced markedly more colonies in COS7 cells as shown in FIGS. 10 a and b . This result was confirmed by three independent experiments. Statistical analysis was conducted according to the Student's t test to determine the significant difference.
  • KRZFPUH-AS4 5′-GGCCTCACCGAGCGCG-3′[SEQ ID NO: 37]or control S-oligonucleotides (KRZFPUH-S4; 5′-CGCGCTCGGTGAGGCC-3′[SEQ ID NO: 38]) using LIPOFECTIN Reagent (GIBCO BRL); and cultured in RPMI1640 supplemented with an appropriate concentration of geneticin for six to twelve days.
  • KRZFPUH-AS4 antisense S-oligonucleotides
  • KRZFPUH-S4 control sense S-oligonucleotides
  • Plasmids expressing KRZFPUH-siRNAs were prepared by cloning double-stranded oligonucleotides into psiU6BX3.0 vector.
  • the oligonucleotides used for KRZFPUH-siRNAs were:
  • the target sequence of siRNA in each of the sequences is underlined.
  • psiU6BX-KRZFPUH psiU6BX-EGFP or psiH1BX-mock plasmid was transfected into cells using FuGENE6 reagent according to the supplier's recommendations (Roche). Total RNA was extracted from the cells 48 hours after the transfection.
  • siRNA short interfering RNA
  • dsRNA 21-mer double-stranded RNA
  • plasmids expressing various KRZFPUH-siRNAs were constructed and examined for their effect on KRZFPUH expression.
  • psiU6BX-KRZFPUH2 but not psiU6BX-KRZFPUH1, psiU6BX-KRZFPUH3 or psiU6BX-KRZFPUH4 significantly suppressed the expression of KRZFPUH in Huh7, Alexander, HepG2 and SNU449 cells ( FIG. 12 and 13 , data not shown).
  • Viable cells transfected with psiU6BX-KRZFPUH2 were markedly reduced compared to those transfected with psiH1BX-KRZFPUH1, psiH1BX-KRZFPUH3, psiH1BX-KRZFPUH4, psiU6BX-EGFP or the control suggesting that decreased expression of KRZPUH suppresses the growth of hepatoma cells ( FIG. 12 and 13 ).
  • the expression profiles of 11 colon cancer tissues were compared with their corresponding non-cancerous mucosal tissues of the colon as in Example 1 using the cDNA microarray containing 23040 genes.
  • This analysis identified a number of genes which expression levels were frequently elevated in cancer tissues compared to their corresponding non-cancerous tissues.
  • a gene with an in-house accession number of B9486, corresponding to the CGI-124/PPIL1 gene (GenBank Accession number: AF151882) was revealed to have enhanced expression levels in the cancer tissues compared to their corresponding non-cancerous mucosae in a magnification range between 2.36 and 4.68 in all six cases that passed the cut-off filter ( FIG. 14 a ).
  • expression of these transcripts in additional colon cancer samples was examined by semi-quantitative RT-PCR as in Example 1 using primers:
  • plasmid expressing myc-tagged PPIL1 protein (pcDNA3.1myc/His-PPIL1) was carried out.
  • the plasmid was constructed as follows. First, total RNA was extracted with Qiagen RNeasy kit (Qiagen) or Trizol reagent (Life Technologies, Inc.) according to the manufacturers' protocol. Ten-microgram aliquot of total RNA were reverse transcribed into cDNAs using poly dT 12 - 18 primer (Amersham Pharmacia Biotech) with Superscript II reverse transcriptase (Life Technologies).
  • RT-PCR was conducted using GeneAmp PCR system 9700 (Perkin-Elmer, Foster City, Calif.) under following condition: denaturing at 94° C. for 4 min; 28 cycles of 94° C. for 30 s, 56° C. for 30 s, and 72° C. for 45 s.
  • the amplified fragment was inserted into pcDNA3.1myc/His (Invitrogen) vector. Then the constructed pcDNA3.1myc/His-PPIL1 was transfected into NIH3T3 cells.
  • pcDNA3.1myc/His-PPIL1 induced markedly more colonies in NIH3T3 cells compared with control plasmids, pcDNA3.1myc/His-LacZ or pcDNA3.1myc/His-asPPIL1, that express the complementary strand of PPIL1 ( FIG. 16 a ).
  • HCT116 human colon cancer cells (ATCC, Rockville, Md.) that express low amount of endogenous PPIL1 were used as cells to be transfected with pcDNA3.1myc/His-PPIL1.
  • pcDNA3.1myc/His-PPIL1 pcDNA3.1myc/His-PPIL1.
  • control sense oligonucleotide PPIL1-S2 5′-CTTCGCTATGGCGGCA-3′ [SEQ ID NO: 43]
  • scramble S-oligonucleotide PPIL1-SCR2,5′-GTTGCACAGCGACGCA-3′ [SEQ ID NO: 92].
  • Each of the synthesized oligonucleotides was transfected, using LIPOFECTIN Reagent (GIBCO BRL), into human colon cancer cells SW480 (ATCC, Rockville, Md.), SNU-C4 and SNU-C5 (both from Korea Cell-line bank), which had shown higher levels of PPIL1 expression among examined 11 colon cancer cell lines.
  • SW480 was cultured in Leibovitz's L-15, and SNU-C4 and SNU-C5 in RPMI1640, all medium supplemented with appropriate concentration of geneticin, for six to twelve days. The cells were then fixed with 100% methanol and stained by Giemsa solution.
  • PPIL1-AS2 significantly reduced the expression of PPIL1 compared to control sense (PPIL1-S2) in SNU-C5 cells ( FIG. 17 a ).
  • PPIL1-S2 control sense
  • FIG. 17 b the number of surviving cells transfected with PPIL1-AS2 was significantly fewer than that with controls, PPIL1-S2 or scramble S-oligonucleotides (PPIL1-SCR2), suggesting that suppression of PPIL1 reduced growth and/or survival of transfected cells ( FIG. 17 b ). Consistent results were obtained in three independent experiments.
  • 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay was additionally carried out to measure the growth-inhibitory effect of PPIL1-AS2 in SW480, SNU-C4 and SNU-C5 cells.
  • MTT 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
  • the cells were lysed by the addition of 1 ml of 0.01 N HCl/10% SDS and the absorbance of lysates was measured with ELISA plate reader at a test wavelength of 570 nm (reference, 630 nm).
  • the cell viability was represented by the absorbance compared to that of control cells.
  • the number of viable cells transfected with PPIL1-AS2 was significantly fewer than that with PPIL1-S2 in these three cell lines ( FIG. 17 c ).
  • PPIL1 protein was hypothesized to be associated with SNW1/SKIP, a human homologue of Snw1, and SnwA. To investigate this hypothesis, pFLAG-PPIL1 expressing Flag-tagged PPIL1 protein was constructed.
  • the entire coding region of PPIL1 was amplified as in Example 15 and the product was cloned into the cloning site of pFLAG-CMV-5c (Sigma) to prepare pFLAG-PPIL1.
  • the entire coding region of SNW1 was amplified by RT-PCR using gene specific primer set: 5′-TGGGAAQTTCCGGAAGAAGATGGCGCTCACCAGC3′ (forward) [SEQ ID NO: 45] and 5′-GTGCCTCGAGCTTCCTCCTCITCITGCCTTCATGC-3′ (reverse) [SEQ ID NO: 46]; and cloned into the cloning site of pcDNA3.1myc/His (Invitrogen) to construct pcDNA3.1myc-SNW1 that expresses myctagged SNW1.
  • pFLAG-PPIL1 was transfected either with or without pcDNA3.1myc-SNW1 into COS7 cells (ATCC, Rockville, Md
  • Proteins were separated by 10% SDS-PAGE and immunoblotted with mouse anti-myc antibody (SANTA CRUZ). HRP-conjugated goat anti-mouse IgG (Amersham) served as the secondary antibody for the ECL Detection System (Amersham).
  • the cells were covered with 2% BSA in PBS for 24 h at 4° C. to block non-specific hybridization.
  • 1:1000 diluted mouse anti-myc monoclonal antibody (Sigmia) or 1:2000 diluted mouse anti-FLAG antibody (Sigma) was used for the first antibody, and the reaction was visualized after incubation with Rhodamine-conjugated anti-mouse second, antibody (Leinco and ICN). Nuclei were counter-stained with DAPI. Fluorescent images were obtained under an ECLIPSE E800 microscope.
  • Multi-tissue northern blot analysis using PPIL1 cDNA as a probe was conducted. Specifically, human multiple-tissue blots (Caontech, Palo Alto, Calif.) were hybridized with a 32 P-labeled PCR product of PPIL1. Pre-hybridization, hybridization, and washing were performed according to the supplier's recommendations. The blots were autoradiographed with intensifying screens at ⁇ 80° C. for 24 to 72 h.
  • the result showed ubiquitous expression of a 1.7 kb transcript expressed.
  • abundant expression was observed in the heart, skeletal muscle, testis, thyroid and adrenal gland ( FIG. 20 ).
  • Plasmids expressing various PPIL1-siRNAs were constructed to examine their effect on PPIL1 expression.
  • psiH1BX3.0 vector was constructed similarly to Example 6. Further, the control vector psiH1BX-EGFP was also prepared as in Example 6. Then, plasmids expressing PPIL1-siRNAs were prepared by cloning double-stranded oligonucleotides into the BbsI site of the psiH1BX3.0 vector. The oligonucleotides cloned into the vector was as follows:
  • the target sequence of siRNA in each of the sequences is underlined.
  • psiH1BX-PPIL-A but not psiH1BX-PPIL-B or psiH1BX-PPIL-C significantly suppressed expression of PPIL1 in SNUC4 as well as SNUC5 cells ( FIG. 21A ).
  • SNUC4 and SNUC5 cells were transfected with psiH1BX-PPIL-A, psiH1BX-PPIL-B, psiH1BX-PPIL-C or a control psiH1BX-EGFP.
  • Viable cells transfected with psiH1BX-PPIL-A were markedly reduced compared to those transfected with psiH1BX-PPIL-B, psiH1BX-PPIL-C, or psiH1BX-EGFP, suggesting that decreased expression of PPIL1 suppressed growth of colon cancer cells ( FIG. 21B ).
  • recombinant protein of PPIL1 was prepared.
  • the entire coding region of PPIL1 was amplified by RT-PCR with a set of primers, 5′-CGCCGGATCCGCTATGGCGGCAATTCCCCCAG-3′ [SEQ ID NO: 53] and 5′-AGCACTCGAGCCCAGAAGGGTATGCCTTAATGATC-3′ [SEQ ID NO: 54].
  • the product was purified, digested with BamHl and Xhol, and cloned into an appropriate cloning site of pGEX-6P-1 (pGEX-PPIL1) or pET21a (pET-PPIL1) vector.
  • pGEX-PPIL1 or pET-PPIL1 was transformed into E. coli DH10B or BL21 codon plus cells. Recombinant protein was induced by the addition of IPTG, and purified from the extracts according to the manufacturers' protocols. When the plasmids were transformed into E. coli cells, production of recombinant protein at the expected size on SDS-PAGE could be observed ( FIGS. 22A and B).
  • PPIL1-interacting proteins were searched using bacterial two-hybrid screening system.
  • the bacterial two-hybrid assay was performed with the BacterioMatch Two-Hybrid System (Stratagene) according to the manufacturer's protocols.
  • the entire coding sequence of PPIL1 obtained as in Example 21 was cloned into the BamHl-Xhol site of pBT vector as bait and screened a human fetal brain cDNA library (Stratagene).
  • stathmin showed an interaction with PPIL1 by simultaneous transformation with pBT-PPIL1 and pTRG-STMN in bacteria ( FIG. 23A ).
  • COS7 cells were transfected pFLAG-PPIL1 expressing FLAG-tagged PPIL1 prepared as in Example 17, and pCMV-HA-STMN expressing HA-tagged stathmin protein, or their combination, were washed with PBS and lysed in NET-N buffer containing 150 mM NaCl, 1% NP-40, 10 mM Tis-HCl pH8.0, 1 mM EDTA, and 1 ⁇ complete Protease Inhibitor Cocktail (Roche).
  • stathmin As described above, the association between FLAG-tagged PPIL1 protein and HA-tagged stathmin protein in vivo was proven by the immunoprecipitation assay in COS7cells ( FIG. 23B ). Interestingly, Western blot analysis using anti-stathmin antibody revealed two bands corresponding to 18 kDa and 20-kDa protein, suggesting the existence of modified form(s) of stathmin. Since stathmin was shown to have putative serine/threonine phosphorylation sites (Ser16, Ser25, Ser38 and Ser63), the larger band may correspond to the phosphorylated form of stathmin. Furthermore, since the immunoprecipitation with anti-Flag antibody showed a single band corresponding to the 20-kDa protein, PPIL1 may associate with the modified form or increase the modification of stathmin by binding with it.
  • pFLAG-PPIL1 and PCMV-HA-STMN were co-transfected into COS7 cells as in Example 22 to examine their subcellular localization by immunohistochemical staining ( FIG. 24 ). Staining with anti-FLAG antibody revealed that the Flag-tagged PPIL1 localized both in the nucleus and cytoplasm, while that with anti-HA antibody demonstrated that HA-tagged stathmin co-localized with PPIL1 in the cytoplasm. This data supports the view of the interaction between PPIL1 and stathmin in the cytoplasm.
  • immunoprecipitation assay was performed similar to Example 22 using various deletion mutants of pCMV-HA-STMN and wild-type pFLAG-PPIL1 to clarify the responsible region for the interaction.
  • the deletion mutants of STMN was amplified using primer sets,
  • a deletion mutant (Del3) lacking amino acids 1-43 of stathmin was able to associate with PPIL1 but a mutant lacking 1 to 65 (Del 4) failed. Meanwhile, another mutant containing amino acids 1 to 61 was capable for the binding ( FIGS. 25A and B), indicating that a region encompassing between codons 44 and 61 is crucial for the binding.
  • mutants (Ser substituted with Ala) were prepared using QuikChange site-directed mutagenesis kit (Stratagene) and primer sets,
  • Colorectal carcinogenesis involves impaired regulation of ⁇ -catenin/Tcf pathway as an early step. Therefore, downstream genes of this pathway were searched in the next procedure.
  • the transduction of APC reduces the level of ⁇ -catenin in the nucleus and subsequently represses the transactivating activity of ⁇ -catenin/Tcf complex in colon cancer cells (van der Heyden et al.,. J Cell Sci 111: 1741-9 (1998)).
  • expression profiles of SW480 cells in which a large amount of ⁇ -catenin is accumulated in nuclei and cytoplasm were compared using microarray method similar as in Example 1.
  • Ad-APC wild-type APC
  • Ad-LacZ LacZ
  • Leibovitz's L-15 72 h after the infection, total RNA was extracted from the cells, and T7-based RNA amplification was carried out using polyA RNA purified from the extracts according to Satoh et al. (Nat Genet 24: 245-50 (2000)).
  • RNA amplified RNA from SW480 cells with Ad-APC and Ad-LacZ were labeled with Cy5-CTP and Cy3-dCTP, respectively, and equal amount thereof were subjected as probes for co-hybridization on microarray slides.
  • the expression profile of 23040 genes in SW480 cells infected with Ad-APC to that with Ad-LacZ was compared to identify a number of genes whose expression levels were down-regulated by the transfection of APC.
  • a gene with an in-house accession number of B7323N corresponding to an EST, Hs.20665 of UniGene cluster in NCBI (the National Center for Biotechnology Information), whose expression level was decreased approximately 4-fold in response to Ad-APC compared to Ad-LacZ was identified.
  • PCR amplification by standard RT-PCR experiment was conducted using following primers: forward, 5′-GGATCATCTATCGGTCAGACG-3′ [SEQ ID No: 73]; and reverse; 5′-TGGGTCACATCCTGCTGGATG-3′ [SEQ ID NO: 74].
  • the amplification was conducted using GeneAmp PCR system 9700 (Perkin-Elmer, Foster City, Calif.) under following condition: denaturing at 94° C. for 4 min; 30 cycles of 94° C. for 30 s, 56° C. for 30 s, and 72° C. for 45 s.
  • the cells were also treated with Ad-Axin, adenovirus expressing wild-type ANV1 that also down-regulated the activity of ⁇ -catenin/Tcf-4 complex, and examined for their expression of B7323N.
  • Ad-Axin adenovirus expressing wild-type ANV1 that also down-regulated the activity of ⁇ -catenin/Tcf-4 complex
  • the cDNA consisted of 2607 nucleotides with an open reading frame of 1542 nucleotides encoding a putative 514 amino acid protein with a predicted molecular weight of 58.8 kD (GenBank accession No. AB104887).
  • the predicted APCDD1 protein had 31% identity with the endo-1,4-beta-xylanase of Thermobacillus xylanilyticus .
  • Motif searches using the computer programs SMART http://smart/embl-heidelberg/de/
  • PSORT II Prediction http://psort nibb.acjp/form2.html
  • APCDD1 down-regulated by APC 1).
  • Comparison of the cDNA sequences with the genomic sequence allowed determining the genomic structure of APCDD1, which consisted of 5 exons and approximately covered a 40-kb genomic region (data not shown).
  • the determined nucleotide sequence of APCDD1 and its predicted amino acid sequence are shown in SEQ ID NOs: 7 and 8, respectively.
  • Example 2 Northern blot, analysis, was conducted as in Example 2 for APCDD1.
  • the Northern blot analysis demonstrated that a 2.6-kb transcript of APCDD1 was expressed abundantly in heart, pancreas, prostate, and ovary but scarcely expressed in lung, liver, kidney, spleen, thymus, colon, and peripheral leukocytes ( FIG. 27 b ).
  • reporter plasmid P1 containing two putative, Tcf/LEF binding motifs TMM1 and 2 with/without an activated form of mutant ⁇ -catenin and wild-type Tcf4 were transfected into HeLa cells ( FIG. 28 a ). More specifically, a putative transcriptional initiation site. (TIS) of APCDD1 was determined by a comparison between a human genomic sequence (GenBank accession No. NT — 019631.4) and the sequence of APCDD1 cDNA.
  • APCDD1 Three fragments of the 5′ flanking region of APCDD1 were amplified by PCR (P1, P2, and P3), and cloned into an appropriate enzyme site of pGL3-Basic vector (Promega). Site directed mutagenesis were performed using QuickChangeTM Site-Directed Mutagenesis Kit (STRATAGENE) for P1 and P2 that contained one or two putative Tcf/LEF binding motifs.
  • STRATAGENE QuickChangeTM Site-Directed Mutagenesis Kit
  • mutant ⁇ -catenin was prepared by RT-PCR using a set of primers, 5′-AAGGATCCGCGTGGACAATGGCTACTCAAG-3′ [SEQ ID NO: 76] and 5′-GGACTCGAGACAGGTCAGTATCAAACCAGGCCAG-3′ [SEQ ID NO: 77] and RNA extracted from HCT116 colon cancer cells as a template, and subsequently cloned into an appropriate cloning site of pcDNA3.1 plasmid vector (Invitrogen).
  • TcfF1 Human cDNA fragments of the entire coding region and its 5′deleted region of Tcf-4 (wtTcf4, dnTcf4) were amplified by RT-PCR using sets of primers TcfF1: 5′-AAGAATTCTGCTGGTGGGTGAAAAAAAAATGC-3′ [SEQ ID NO: 78] and TcfR1: 5′-CTACTCGAGTTCTAAAGACTTGGTGACGAGCGAC-3′ [SEQ ID NO: 79], and TcfF3: 5′-AGGAATTCGTGCATCATGGTCCCACCACATCATAC-3′ [SEQ ID NO: 80] and TcfR1, respectively.
  • the products were also cloned into the pcDNA3.1 plasmid vector.
  • the reporter activity of plasmid P1 was significantly enhanced by the introduction of the activated form of ⁇ -catenin and wild-type Tcf4 ( FIG. 28 b ). Interestingly, the enhanced activity was reduced when P1 was co-transfected with the dominant-negative form of Tcf4, suggesting that Tcf4 affected the promoter activity of APCDD1.
  • the promoter activity for each of the various deletion mutants of P1 was further compared.
  • the activity of P1 was significantly higher than that of P2 and P3 respectively, and the activity of P2 containing only TBM2 was significantly higher than that of P3 ( FIG. 28 b ).
  • These data suggested that a region encompassing ⁇ 971 and ⁇ 151 may associate with the catenin/Tcf4 complex, and is involved in the APCDD1 promoter activity. Since this region contained two possible Tcf/LEF-binding motifs, these motifs were hypothesized to be responsible for the transcriptional activation.
  • reporter plasmids P1M and P2M in which the candidate Tcf/LEF-binding motif was changed to CTTTG GC [SEQ ID NO: 81] to which ⁇ -catenin/Tcf4 complex was unable to bind were constructed.
  • Reporter assay using these five plasmids revealed that the P1M and P2M fragment containing the mutated motif had decreased ability to activate transcription of APCDD1; and its luciferase activity was equivalent to that of the P2 or P3 fragment ( FIG. 28 b ).
  • an electrophoretic mobility shift assay was carried out using oligonucleotides designed to encompass the TBM1 sequence (APCDD1-TBM1) and the TBM2 sequence (APCDD1-TBM2). Specifically, EMSA was performed using extracts from intact nuclei of SW480 cells as previously described (van der Heyden et al., J Cell Sci 111: 1741-9 (1998)).
  • Two double-stranded 16-nucleotide DNA probes were prepared by annealing FF (5′-GCTTTGATTGTGGTGA-3′ [SEQ ID NO: 82]) and RR (5′-TCACCACAATCAAAGC-3′ [SEQ ID NO: 83]) for APCDD1-TBM1, and FF2 (5′-CCCCTTTGAACACCTT-3′ [SEQ ID NO: 84]) and RR2 (5′-AAGGTGTTCAAAGGGG-3′ [SEQ ID NO: 85]) for APCDD1-TBM2.
  • APCDD1 plasmids expressing APCDD1 (pcDNA-APCDD1) and complementary strand of APCDD1 (pcDNA-antisense) were prepared to carry out a colony formation assay in LoVo cells (ATCC, Rockville, Md.) expressing low amount of APCDD1. More specifically, the entire coding region of APCDD1 was amplified by RT-PCR using gene specific primer set: 5′-GCGGAATTCAGGGCCCAGAGCAGGACTG-3′ [SEQ ID NO: 86] and 5′-TAGCTCGAGCTAAAACTTCTATCTGCGGATGT-3′ [SEQ ID NO: 87].
  • PCR product was cloned into appropriate cloning site of pcDNA3.1 (Invitrogen). Then, LoVo cells were transfected with either the constructed pcDNA-APCDD1 or pcDNA-antisense, and the cells were incubated in HAM's F-12 supplemented with an appropriate concentration of geneticin for 10 to 21 days. The cells were fixed with 100% methanol and stained with Giemsa solution.
  • LoVo cells expressing exogenous APCDD1 LoVo-APCDD1 cells were established to compare their growth with control cells transfected with mock vector ( FIG. 30 b ). LoVo-APCDD1 cells grew at a markedly increased rate compared to the control LoVo-mock cells ( FIG. 30 c ).
  • APCDD1-AS2 significantly suppressed the expression of APCDD1 compared to control APCDD1-S1 in the cells ( FIG. 31 a ).
  • introduction of APCDD1-AS2 clearly suppressed focus formation of the cells, compared with APCDD1-S2, suggesting that suppression of APCDD1 reduces growth and/or survival of transfected cells ( FIG. 31 b ).
  • MIT assay confirmed decreased cell survival in response to APCDD1-AS2 compared to APCDD1-R2, APCDD1-Sc2, and untreated cells ( FIG. 31 c );
  • polyclonal antibody against APCDD1 was prepared as follows. First, recombinant His-tagged APCDD1 protein was produced in E. coli and purified from the cells using Pro BondTM histidine Resin (Invitrogen) according to the manufacturer's recommendations. The recombinant protein was used for the immunization of rabbits. The polyclonal antibody against APCDD1 was purified from the sera. For western blot analysis, proteins were separated by 10% SDS-PAGE and immunoblotted with anti-APCDD1 antibody. HRP-conjugated goat anti-rabbit IgG (Santa Cruz Biotechnology) served as the secondary antibody for the ECL Detection System (Amersham Pharmacia Biotech).
  • Immunohistochemical staining of SW480 cells and frozen tissues was also carried out as described in Example 18 using anti-APCDD1 antibody.
  • Paraffin-embedded tissue sections were subjected to the SAB-PO peroxidase immunostaining system (Nichirei, Tokyo, Japan) according to the manufacturer's recommended method.
  • Antigens were retrieved from deparaffinized and re-hydrated tissues by pre-treating the slides in citrate buffer (pH6) in a microwave oven for 10 min at 700 W.
  • Western blot analysis with anti-APCDD1 antibody using extracts of colon cancer cells, including HCT116, SNUC4, and SW480 showed 58-kDa bands corresponding to APCDD1 ( FIG. 32 ).
  • the size of endogenous APCDD1 protein was quite similar to that of exogenous Flag-tagged APCDD1 protein detected with anti-FLAG antibody.
  • the expression of APCDD1 was most abundant in SW480 cells among the three colon cancer cell lines.
  • APCDD1 fluorescent immunohistochemical staining of APCDD1 was carried out using SW480 cells. Cells were fixed, stained with anti-APCDD1, and visualized with fluorescein conjugated secondary antibody. Signals were observed at the cell-to-cell boundaries and cytoplasms ( FIG. 33 ).
  • APCDD1 expression in non-cancerous colonic mucosae and carcinoma tissues were also investigated and staining were revealed in the cytoplasms of the non-cancerous and cancerous cells ( FIG. 34 ). Notably, strong signals were observed at the apical boarder of epithelial cells.
  • novel human genes WDRPUH and KRZFPUH are markedly elevated in hepatocellular carcinoma as compared to non-cancerous liver tissues.
  • novel human genes PPZL1 and APCDD1 are markedly elevated in colon cancer cells as compared to non-cancerous tissues. Accordingly, these genes may serve as a diagnostic marker of cancer and the proteins encoded thereby may be used in diagnostic assays therefore.
  • the present inventors have also shown that the expression of novel protein WDRPUH, KRZFPUH, PPIL1, or APCDD1 promotes cell growth whereas cell growth is suppressed by antisense oligonucleotides or siRNAs corresponding to the WDRPUH, KRZFPUH, PPIL1, or APCDD1 gene.
  • WDRPUH, KRZFPUH, PPIL1, or APCDD1 protein stimulates oncogenic activity.
  • this novel oncoprotein is a useful target for the development of anti-cancer pharmaceuticals.
  • agents that block the expression of WDRPUL, KRZFPUH, PPIL1, or APCDD1 or prevent its: activity may find therapeutic utility as anti-cancer agents, particularly anti-cancer agents for the treatment of HCC and colon cancer.
  • anti-cancer agents include antisense oligonucleotides, siRNAs, and antibodies that recognize WDRPUH, KRZFPUH, PPIL1, or APCDD1.
  • stathmin directly associates with stathmin, which result suggests the ability of PPIL1 to enhance phosphorylation of stathmin in vivo. Since stathmin is reported to be involved in the progression of cell cycle and linked to various types of cancer, agents that inhibit the activity of the complex may also find utility in the treatment and prevention of colorectal cancer.

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