# Patent

## Title
Cancer-associated genes

## Abstract

The present invention is related to a DNA comprising a nucleotide sequence encoding a polypeptide represented by SEQ ID NO:1 or SEQ ID NO:2. The DNA according to the present invention is highly expressed in prostatic adenocarcinoma and ovarian carcinoma, and is a cancer-associated gene, so that it is possible to inhibit cancer by blocking the binding of the present protein to its ligand. Accordingly, the present antibody is used not only in the detection of the present protein, but also as an agent for the treatment or prevention of cancers such as prostatic adenocarcinoma and ovarian carcinoma.

## Background
This application is the national phase under 35 U.S.C. § 371 of PCT International Application No. PCT/JP01/11305 which has an International filing date of Dec. 21, 2001, which designated the United States of America.
FIELD OF THE INVENTION
The present invention is related to a novel DNA and a cancer-associated gene comprising the DNA, a recombinant protein encoded by the DNA, an antibody binding to the protein, an anti-cancer agent comprising the antibody, a method of screening a substance that binds to the protein or a peptide fragment thereof.
BACKGROUND OF THE INVENTION
A grand scale sequencing in the Human Genome Project has been producing a lot of information on the nucleotide sequences of human genome every day.
A final goal of the project is not only to determine the whole genomic nucleotide sequences, but also to reveal and understand various human life phenomena based on the information about their structure, i.e., DNA sequence information.
Regions encoding proteins occupy only a small part of the human genome. Although the coding region may recently be predicted by utilizing techniques in information technology such as neural network and hidden markov model, their predictive accuracy is not yet enough.
The present inventors have succeeded in directly cloning a novel DNA comprising a region encoding a protein from cDNA library derived from human adult whole brain, human amygdala, human adult hippocampus, and human fetal whole brain, and in determining its nucleotide sequence, and have completed the present invention.
SUMMARY OF THE INVENTION
A first aspect of the present invention relates to a DNA comprising a nucleotide sequence encoding the following polypeptide (a) or (b):

    
    
        (a) a polypeptide consisting of an amino acid sequence which is identical or substantially identical with an amino acid sequence represented by SEQ ID No. 1 or No. 2,
        (b) a polypeptide consisting of an amino acid sequence represented by SEQ ID No. 1 or No. 2 in which part of amino acids are deleted, substituted or added, and having substantially the same biological activity as the function of the polypeptide (a).
    
    


A second aspect of the present invention relates to a DNA of the following (a) or (b):

    
    
        (a) a DNA comprising a nucleotide sequence encoding an amino acid sequence represented by SEQ ID No. 1 or No. 2 in a nucleotide sequence represented by SEQ ID No. 1 or No. 2,
        (b) a DNA hybridizing with the DNA (a) under stringent conditions and encoding a protein having substantially the same biological activity as the function of the polypeptide consisting of the amino acid sequence in (a).
    
    


The DNAs of the first and second aspects will be also referred to as “the present DNA” in the present specification. The present invention also relates to the gene comprising the present DNAs.
A third aspect of the present invention relates to a protein comprising the following polypeptide (a) or (b):

    
    
        (a) a polypeptide consisting of an amino acid sequence which is identical or substantially identical with an amino acid sequence represented by SEQ ID No. 1 or No. 2,
        (b) a polypeptide consisting of an amino acid sequence represented by SEQ ID No. 1 or No. 2 in which part of amino acids are deleted, substituted or added, and having substantially the same biological activity as the function of the polypeptide (a),

and to a recombinant protein which is obtained by the expression of the gene of the present invention.

    
    


A forth aspect of the present invention relates to various kinds of antibodies binding to the above protein.
A fifth aspect of the present invention relates to various kinds of anti-cancer agents comprising the above antibody.
A sixth aspect of the present invention relates to a method of screening a substance which binds to the above protein or a partial peptide thereof, comprising:

    
    
        (a) bringing a sample to be tested in contact with said protein or partial peptide thereof,
        (b) detecting a binding activity between the sample and said protein or partial peptide thereof, and
        (c) selecting a substance which has a binding activity to said protein or partial peptide thereof.
    
    


The seventh aspect of the present invention relates to a polynucleotide hybridizing with the DNA of Claim 1 or 2 under the stringent conditions and consisting of at least 15 bases.
The eighth aspect of the present invention relates to a method of detecting cancer with the use of the above polynucleotide as a probe, comprising:

    
    
        (a) bringing a sample to be tested in contact with said polynucleotide, and
        (b) detecting a hybridizing activity between the sample and said polynucleotide.
    
    





BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 schematically shows the structures of the proteins of the present invention, “pj01304s1” and “pj01304GS”, and Patched protein of Drosophila. A transmembrane region is painted in black, and an extracellular region is represented in thin dark. FIG. 1 shows the presence of two large extracellular domains.



BEST MODE FOR CARRYING OUT THE INVENTION
[DNA According to the Present Invention]
The present DNA is isolated as cDNA fragment from a cDNA library prepared by the present inventors by using as starting materials mRNAs of human adult whole brain, human amygdala, human adult hippocampus, and human fetal whole brain, are commercially available from Clontech, and identified with determination of its nucleotide sequence.
Thus, clones are randomly isolated from the library derived from human adult whole brain, human amygdala, human adult hippocampus, and human fetal whole brain, which is prepared in accordance with Ohara et al., DNA Research Vol.4, 53-59 (1997).
Next, after removing overlapped clones (clones which will repeatedly appear) with hybridization, the remaining clones are then subjected to transcription and translation in vitro and nucleotide sequences at both ends of clones which express a product with 50 kDa or more are determined.
Homology search is done on database to remove known genes with the use of the nucleotide sequences at both ends thus obtained as a query. The whole nucleotide sequence is determined for a clone which has identified as a novel gene.
In addition to the above screening method, the 3′- and 5′-terminal sequences are aligned with the human genome. And in the case an unknown long-ORF gene is found in a region caught between them, the whole length analysis of cDNA is done for the gene.
Unknown genes, which could not be obtained by conventional cloning techniques depending on known ones, can now be systematically cloned in this way.
Paying much attention not to make any artificial errors in short fragments or determined sequences, the whole region of human genes comprising the present DNA may be prepared by using PCR methods such as RACE.
A clone (KIAA1742) comprising the present DNA may be obtained accordingly. The function, etc. of a protein encoded by a gene in the clone is disclosed in the present specification.
The present DNA may be alternatively cloned by preparing a synthetic DNA primer with an appropriate nucleotide sequence such as a part of the polypeptide of the present invention, and amplifying it with an appropriate library by means of PCR. The present DNA may be further selected from DNAs integrated into appropriate vectors by means of hybridization with a DNA fragment or synthetic DNA encoding the whole region or part of the present polypeptide.
Hybridization may be performed in accordance with a method described in, for example, Current protocols in molecular biology (edited by Frederick M. Ausubel et al., 1987). If a commercial library is used it may be done according to a method described in instructions attached thereto.
The present DNA may be any DNA as long as it consists of a nucleotide sequence which encodes the polypeptide of the present invention, including a cDNA identified and isolated from cDNA libraries derived from human brain and other tissues or cells such as heart, lung, liver, spleen, kidney and testis, and a synthetic DNA.
A vector, which is used in the preparation of the libraries, includes bacteriophage, plasmid, cosmido and phagemid. The cDNA may be also amplified by means of Reverse Transcription coupled Polymerase Chain Reaction (RT-PCR) with the use of a total RNA or mRNA fraction prepared from the above tissues or cells.
An “amino acid sequence which is substantially identical with an amino acid sequence represented by SEQ ID No. 1 or No. 2” means an amino acid sequence having homology on an average of about 70% or more, preferably about 80% or more, more preferably about 90% or more, further more preferably about 95% or more to the whole amino acid sequence represented by SEQ ID No. 1 or No. 2.
Thus, the polypeptide consisting of the amino acid sequence which is substantially identical with the amino acid sequence represented by SEQ ID No. 1 or No. 2 includes a polypeptide having the above homology to the amino acid sequence represented by SEQ ID No. 1 or No. 2 and having substantially the same biological activity (or function) as the function of a polypeptide consisting of the above amino acid sequence. The term “substantially the same” means the activities or functions of the both substances are the same with each other in quality or property.
The present polypeptide includes a polypeptide consisting of the amino acid sequence represented by SEQ ID No. 1 or No. 2 in which part of amino acids (preferably 1 ̃20, more preferably 1 ̃10, further more preferably a few amino acids) are deleted, substituted or added, and having substantially the same biological activity (or function) as the function of the polypeptide consisting of the amino acid sequence represented by SEQ ID No. 1 or No. 2.
The DNA encoding the polypeptide consisting of the amino acid sequence which is substantially identical with the amino acid sequence represented by SEQ ID No. 1 or No. 2, or the polypeptide consisting of the amino acid sequence represented by SEQ ID No. 1 or No. 2 in which part of amino acids are deleted, substituted or added may be easily prepared by well known methods such as site-specific mutation, genetic homologous recombination, primer extension method and PCR, or any optional combinations thereof.
In order for the polypeptide or protein to have substantially the same biological activity, it is possible to make a substitution among amino acids belonging to the same group (polar, non-polar, hydrophobic, hydrophilic, positive-charged, negative-charged, or aromatic amino acid group) in the amino acids that constitute the present polypeptide. Alternatively, it is desirable to keep amino acids which are included in a functional domain.
Furthermore, the present DNA includes the DNA comprising a nucleotide sequence encoding the amino acid sequence represented by SEQ ID No. 1 or No. 2 in the nucleotide sequence represented by SEQ ID No. 1 or No. 2, and the DNA hybridizing with said DNA under stringent conditions and having substantially the same biological activity as the function of the polypeptide consisting of the amino acid sequence represented by SEQ ID No. 1 or No. 2.
The DNA that hybridizes with the DNA comprising the nucleotide sequence encoding the amino acid sequence represented by SEQ ID No. 1 or No. 2 in the nucleotide sequence represented by SEQ ID No. 1 or No. 2 under stringent conditions includes a DNA having homology on an average of about 80% or more, preferably about 90% or more, more preferably about 95% or more to the whole nucleotide sequence represented by SEQ ID No. 1 or No. 2.
Hybridization may be performed in accordance with a method described in, for example, Current protocols in molecular biology (edited by Frederick M. Ausubel et al., 1987). If a commercial library is used it may be done according to a method described in instructions attached thereto.
The phrase “stringent conditions” in this specification means conditions under which Southern blot hybridization is carried out in an aqueous solution containing 1 mM NaEDTA, 0.5M Na2HPO4 (pH 7.2) and 7% SDS at 65° C., followed by the washing of a membrane with an aqueous solution containing 1 mM NaEDTA, 40 mM Na2HPO4 (pH 7.2) and 1% SDS at 65° C.
The present DNA thus cloned may be directly used, or optionally digested with a restriction enzyme or tagged with a linker for use. The present DNA may have a translation initiation codon “ATG” at its 5′-end, and a translation termination codon, “TAA”, “TGA” or “TAG” at its 3′ end. These codons may be also added by using an appropriate synthetic DNA adapter.
[Polynucleotide According to the Present Invention]
Since the present DNA (gene) is highly expressed in cancer cells as seen from the following examples, detection of cancer can be done by detecting the gene according to the present invention.
Accordingly, the polynucleotide which hybridizes with the DNA comprising the nucleotide sequence represented by SEQ ID No. 1 or No. 2 under stringent conditions may be used as probe in the above detection of cancer.
The length of the polynucleotide is at least 15 bases, preferably 100 bases or more, more preferably 500 bases or more, further more preferably 1,000 bases or more.
The phrase “stringent conditions” in this specification means conditions under which Southern blot hybridization is carried out in an aqueous solution containing 1 mM NaEDTA, 0.5M Na2HPO4 (pH 7.2) and 7% SDS at 65° C., followed by the washing of a membrane with an aqueous solution containing 1 mM NaEDTA, 40 mM Na2HPO4 (pH 7.2) and 1% SDS at 65° C.
[Protein According to the Present Invention]
The protein according to the present invention may be easily prepared by any method known to those skilled in the art, by constructing an expression vector comprising the present DNA or the gene comprising thereof, culturing a transformant transformed with the expression vector to produce and accumulate the present polypeptide or a recombinant protein comprising thereof, and collecting them.
The expression vector may be constructed by any known method in the art. For example, it is made by (1) excising a DNA fragment containing the present DNA or the gene comprising the DNA, and (2) ligating the DNA fragment downstream of a promoter in the expression vector.
Vectors to be used in the present invention include those derived from Escherichia coli such as pBR322, pBR325, pUC18, pUC118; those derived from Bacillus subtilis such as pUB110, pTP5 and pC194; those derived from yeast such as pSH19 and pSH15; bacteriophage such as λphage; animal viruses such as retorovirus, vaccinia virus and baculovirus.
Promoters to be used in the present invention may be any promoters suitable for a host cell which is used in the expression of the gene, including, for example, trp promoter, lac promoter, recA promoter, λPL promoter and lpp promoter for E. coli; SPO1 promoter, SPO2 promoter and penP promoter for Bacillus subtilis; PHO5 promoter, PGK promoter, GAP promoter and ADH promoter for yeast; and SRα promoter, SV40 promoter, LTR promoter, CMV promoter and HSV-TK promoter for animal cells.
Other elements known in the art such as an enhancer, a splicing signal, a polyadenylation signal, a selection marker and SV40 replication origin may be added to the expression vectors. The protein encoded by the present DNA may be optionally expressed as a fused protein with other proteins such as glutathione-S-transferase and protein A. The fused protein may be cleaved by an appropriate protease and separated into each protein.
The host cell used in the present invention includes Escherichia, Bacillus, yeast, insect cells, and animal cells.
The examples of Escherichia include E. coli K-12·DH1 (Proc. Natl. Acad. Sci., USA, vol. 60 160 (1968)), JM103 (Nucleic Acids Research, vol. 9, 309 (1981)), JA221 (Journal of Molecular Biology, vol. 120, 517 (1978)) and HB101 (Journal of Molecular Biology, vol. 41, 459 (1969)).
The examples of Bacillus include Bacillus subtilis MI114 (Gene vol. 24, 255 (1983)), and 207-21(Journal of Molecular Biology, vol. 95, 87 (1984)).
The examples of yeast include Saccaromyces cerevisiae AH22, AH22R-, NA87-11A, DKD-5D, and 20B-12; Schizosaccaromyces pombe NCYC1913, NCYC2036; and Saccaromyces picjia pastoris.
The examples of animal cells include simian cell COS-7, Vero, Chinese hamster cell CHO (“CHO cell”), dhfr gene-defective CHO cell, mouse L cell, mouse AtT-20 cell, mouse myeloma cell, rat GH3 cell and human FL cell.
The transfomation of these cells may be carried out in accordance with a method known in the art such as those described in the following articles:
Proc. Natl. Acad. Sci., USA vol. 69, 2110 (1972); Gene, vol. 17, 107(1982), Molecular & General Genetics, vol. 168, 111 (1979); Methods in Enzymology, vol. 194, 182-187 (1991); Proc. Natl. Acad. Sci., USA vol. 75, 1929 (1978); Cell Engneering, additional volume 8, “New Cell Engineering experimental protocols, 263-267 (published by Shu-junn Co.); and Virology vol. 52 456 (1973).
The transformant thus transformed with the expression vector comprising the present DNA or the gene comprising thereof may be cultured according to a method known in the art.
Escherichia host cells may be normally cultured at about 15 ̃43° C. for about 3 ̃24 hours with aeration and stirring, if necessary. Bacillus host cells may be normally cultured at about 30 ̃40° C. for about 6 ̃24 hours with aeration and stirring, if necessary.
Yeast host cells may be normally cultured in a culture medium with pH about 5 ̃8 at about 20 ̃35° C. for about 24 ̃72 hours with aeration and stirring, if necessary.
Animal host cells may be normally cultured in a culture medium with pH about 6 ̃8 at about 30 ̃40° C. for about 15 ̃60 hours with aeration and stirring, if necessary.
The polypeptide or protein according to the present invention may be isolated and purified from the above culture as follows. After the completion of culturing, bacteria or cells are collected by a known method, suspended in an appropriate buffer solution, and destroyed by means of ultrasonic, lysozyme and/or freezing and thawing treatment, followed by centrifugation or filtration to give a crude protein extract. The buffer solution may contain a protein-denaturing agent such as urea and guanidine hydrochloride, or a surfactant such as TritonX-100TM. If the protein is secreted into the culture medium, the bacteria or cells are separated from its supernatant by a known method after the completion of culturing, and the resulting supernatant is collected. The protein thus obtained and contained in the culture supernatant or extract may be purified by an appropriate combination of known separation and purification methods.
The present polypeptide or protein thus obtained may be converted into their salt form, which may be converted into its free from vice versa or into other salt forms according to a known method. The protein produced by the transformant may be treated with an appropriate protein-modifying enzyme such as trypsin or chymotrypsin in order to optionally add modification to it or to partially remove polypeptide from it before or after purification.
The presence of present polypeptide or protein or salt thereof may be determined by various binding assay methods or enzyme immunoassay using a specific antibody.
[Antibody According to the Present Invention]
There is no limitation in the present antibody as long as it binds to the protein according to the present invention. It may be obtained as a polyclonal antibody or monoclonal antibody by a known method. A preferable example of the present antibody is a monoclonal antibody derived from mammalian, which contains the one produced by a hybridoma and the one produced by a host cell which has been transformed by genetic engineering technique with an expression vector comprising a gene encoding the antibody. It is preferable that the present antibody specifically binds to the present protein.
The hybridoma producing the monoclonal antibody may be prepared with the use of a known technique. Thus, it is prepared by doing immunization with the present protein as a sensitizing antigen by a known method, fusing the resulting immunocyte with a known parent cell by a known cell fusion method, and screening a monoclonal antibody-producing cell by a known screening method. More specifically, the monoclonal antibody is prepared as follows.
A gene sequence encoding the present protein is inserted into a known expression vector system and an appropriate host cell is transformed with the vector, followed by purification of a desired protein from the host cell or a culture supernatant.
Next, the resulting protein is used as the sensitizing antigen. Alternatively, a partial polypeptide of the present protein, which may be usually obtained by a chemical synthesis method known to those skilled in the art based on the amino acid sequence of the present protein, is also used as the sensitizing antigen.
The partial polypeptide of the present protein includes those which have at least 10 amino acids or more, preferably at least 50 amino acids or more, more preferably at least 70 amino acids or more, further more preferably at least 100 amino acids or more, most preferably 200 amino acids or more of the amino acid sequence constituting the present protein, and the polypeptide have substantially the same biological activity with the function of the polypeptide according to the present invention. The partial polypeptide preferably comprises a functional domain, which will be described hereinafter. Although the C-end of the partial polypeptide is usually a carboxyl group (—COOH) or a carboxylate group (—COO—), it may be also an amide group (—CONH) or an ester group (—COOR) as it is for the present protein. The N-end of the partial polypeptide includes the one in which an amino group of methionine is protected with a protecting group, the one having a glutamyl group formed by cutting of the N-end in a body and subjected to pyroglutamic acid oxidation, the one in which a substituted group in the side chain of an amino acid is protected with an appropriate protecting group, and a complex peptide such as a glycopeptide in which a sugar chain is coupled.
The present antibody may be used in the detection and purification, etc. of the present protein. Since the present gene is expressed in a high degree in cancer cells as described in the Examples, the present antibody that is coupled with a radio isotope, a chemotherapeutic agent, toxins derived from bacteria can inhibit the growth of the cells. An epitope existing on the present protein, which can be recognized by the present antibody, is not limited to any particular one. Accordingly, any fragment may be used as the antigen in the preparation of the present antibody, as long as it comprises the epitope existing on the present protein.
The animal to be immunized with the sensitizing antigen is not limited to a particular one, but is usually selected in view of compatibility with the parent cell used in the cell fusion, including rodent such as mouse, rat and hamster.
The animal may be immunized with the sensitizing antigen by a known method, usually by intraperitoneal or subcutaneous injection. More specifically, the sensitizing antigen appropriately diluted and suspended in PBS (Phosphate-Buffered Saline) or physiological saline is appropriately mixed with a usual adjuvant such as Freund's complete adjuvant, emulsified and administered to the animal several times at an interval of 4-12 days. An appropriate carrier may be used in the immunization.
After the increase of an antibody level in serum of the immunized animal is confirmed, the immunocyte is collected and subjected to the cell fusion. A preferable immunocyte, for example, is a spleen cell.
The parent cell to be fused with the immunocyte is myeloma derived from mammalian, which includes various known cell strains such as P3 (P3x63Ag8.653)(J. Immunol. (1979) 123, 1548-1550), P3x63Ag8U.1(Current Topics in Microbiology and Immunology (1978) 81, 1-7), NS-1 (Kohler, G. and Milstein, C. Eur. J. Immunol. (1976) 6, 511-519), MPC-11 (Marguiles, D. H., et al., Cell (1976) 8, 405-415), SP2/0 (Shulman, M. et al., Nature (1978) 276, 269-270), FO (de St., Groth, S. F. et al., J. Immunol. Methods (1980) 35, 1-21), S194 (Trowbridge, I. S. J. Exp. Med. (1978) 148, 313-323), and R210 (Galfre, G. et al., Nature (1979) 277, 131-133).
The cell fusion between the immunocyte and myeloma may be done according to a known method such as that in Kohler, G. and Milstein, C. Methods Enzymol. (1981) 73, 3-46.
More specifically, the cell fusion is carried out in a usual nutritional medium in the presence of a cell fusion-promoting agent such as polyethyleneglycol (PEG) and Sendai virus (Hemagglutinating Virus of Japan: HVJ). An auxiliary agent such as dimethylsulfoxide may be optionally supplemented to increase hybridization efficiency.
A ratio of the amount of immunocyte to that of myeloma may be optionally selected, being preferably 1-10. Culture medium to be used in the cell fusion includes any culture medium which is used for culturing the above cells such as RPMI1640 culture medium and MEM culture medium. A serum-supplementing agent such as Fetal Calf Serum (FCS) may be used together.
Predetermined amounts of the immunocyte and the myeloma are mixed well in the above culture medium. PEG solution (e.g., with an average molecular weight of ca.1000-6000) warmed at about 37° C. in advance is added to a final concentration of 30-60% (w/v), and the cells are then mixed to form a desired hybridoma. After sequential addition of an appropriate culture medium, the process of centrifugation and removal of a supernatant is repeated in order to remove the cell fusion-promoting agent which is disadvantageous to the growth of the hybridoma.
The resulting hybridoma is then selected by being cultured in a usual selection medium such as HAT medium containing hypoxanthine, aminopterin and thymidine. The culture in HAT medium is maintained for enough of time (usually from several days to several weeks) so that non-fused cells (cells other than hybridoma) will die. Then, a hybridoma producing a desired antibody is screened and cloned with a limiting dilution method.
In addition to the immunization of the animal other than human with the antigen to obtain the hybridoma, it is possible to obtain a desired humanized antibody having a binding activity to the present protein by sensitizing human lymphocyte with the present protein in vitro and fusing the sensitized lymphocyte with human myeloma having immortality (Japanese Patent Publication Hei.1 (1989)-59878). Alternatively, a transgenic animal having the repertoire of all the genes for human antibody may be administered with the present protein to give a cell producing the present antibody, followed by the fusion of the resulting cell with an immortalized cell to produce the humanized antibody for the present protein PCT WO94/25585, WO93/12227, WO92/03918, WO94/02602).
The hybridoma thus prepared and producing the monoclonal antibody of the present invention may be maintained in passage culture using a usual medium, or may be stored in liquid nitrogen for a long period of time.
The monoclonal antibody may be obtained from the hybridoma by culturing the hybridoma in a usual method and collecting it from its supernatant, or by administering the hybridoma into its compatible mammalian and obtaining it from its ascites. The former method is suitable for the production of a highly purified antibody, and the latter method for a mass production of the antibody.
According to the present invention, a gene encoding an antibody is cloned from the hybridoma, inserted into an appropriate vector, introduced into the host cell and expressed by means of genetic recombination technique to give a recombinant-type monoclonal antibody (for example, Vandamme, A. M. et al., Eur. J. Biochem. (1990) 192, 767-775).
Specifically, mRNA encodng a variable (V) region of the present antibody is isolated from the hybridoma producing the present antibody, by preparing total mRNA with the use of guanidine-ultracentrifugation (Chirgwin, J. M. et al.Biochemstry (1979) 18, 5294-5299), AGPC method (Chomczynski, P. et al., Anal. Biochem. (1987) 162, 156-159) and the like, and preparing a desired mRNA with the use of mRNA Purification Kit (Pharmacia Co.). Alternatively, mRNA may be directly prepared by means of QuickPrep mRNA Purification Kit (Pharmacia Co.).
A cDNA of the variable (V) region of the present antibody is synthesized with the resulting mRNA by means of a reverse trascriptase. For example, the synthesis of cDNA may be done by using AMV Reverse Transcriptase First-strand cDNA Synthesis Kit (Seikagaku Industry Ltd.). Alternatively, the synthesis and amplification of cDNA may be done by using 5′-Ampli FINDER RACE Kit (Clontech Co.) and 5′-RACE method with PCR (Frohman, M. A. et al., Proc. Natl. Acad. Sci., USA (1988) 85, 8998-9002, Belyavsky, A. et al., Nucleic Acids Res. (1989) 17, 2919-2932), etc.
A desired DNA fragment is purified from the resulting PCR products and ligated with a vector DNA. The resulting expression vector is introduced into E. coli and the like. A colony containing a desired vector is selected and the vector is prepared from the colony. A nucleotide sequence of the desired DNA is confirmed by a known method such as dideoxy nucleotide chain termination method.
The desired DNA encoding the V region of the present antibody is then integrated into another expression vector containing a DNA encoding the constant region (C region) of a desired antibody.
The gene encoding the present antibody is integrated into an expression vector so that it will be expressed under a control of an expression-regulating region such as an enhancer and promoter. The host cell is then transformed with the expression vector to produce the antibody.
For the expression of the antibody, a DNA encoding a heavy chain (H chain) or a light chain (L chain) may be separately integrated into a different expression vector and used together for co-transformation of the host cell, or a DNA encoding both the H chain and L chain may be integrated into a single expression vector and used for transformation of the host cell (WO 94/11523).
Transgenic animals may be also used for the production of the recombinant-type antibody. For example, the gene for the antibody is inserted within a gene encoding a protein secreted specifically into milk (e.g., goat casein) to give a fused gene. A DNA fragment comprising the fused gene is injected into a goat's embryo, which is then introduced into a female goat. The desired antibody may be obtained from milk of a transgenic goat which will be born by the goat having received the embryo or from milk of off-springs of the transgenic goat. Hormones may be optionally administered to the transgenic goat in order to increase an amount of milk comprising the desired antibody (Ebert, K. M. et al., Bio/Technology (1994) 12, 699-702).
In addition to the above antibodies, various genetic recombinant-type antibodies, which have been artificially modified in order to decrease heteroantigenecity against human, such as a chimera antibody and a humanized antibody may be used in the present invention.
The chimera antibody may be obtained by ligating the above DNA encoding the V region of the antibody with a DNA encoding the C region of a human antibody, integrating the resulting DNA into an expression vector, and introducing the vector into a host cell to produce it. The useful chimera antibody according to the present invention may be prepared according to these conventional methods.
The humanized antibody is also referred to as “reshaped humanized antibody”, which is obtained by transplanting the CDR (complementary determining region) of an antibody from mammalian other than human, such as mouse into the CDR of a human antibody. A general technique of genetic recombination for the humanized antibody is also known (European Patent Application EP125023, WO96/02576).
Specifically, a DNA, which is designed so that it can ligate CDR of the mouse antibody with the framework (FR) region of the human antibody, is synthesized with the use of PCR by using as primer a few oligonucleotides having a part overlapping the end regions of both CDR and FR (WO98/13388).
The FR regions linked together through CDRs are selected so that the CDRs will constitute an excellent antigen-binding site. Amino acids in the FR of the V region of the antibody may be substituted, where necessary, so that the CDRs in the reshaped humanized antibody will form an appropriate antigen-binding site (Sato, K. et al., Cancer Res. (1993) 53, 851-856).
The C region in the chimera or humanized antibodies is derived from the human antibody, such as CH1, CH2, CH3, and CH4, for the H chain, and Cκ and Cλ for the L chain. The C region of the human antibody may be modified in order to improve stability of the antibody itself or the production thereof.
The chimera antibody consists of the variable region of antibodies derived from mammalian other than human and the constant region of the human antibody. On the other hand, the humanized antibody consists of the CDR of antibodies derived from mammalian other than human, and the FR region and the constant region of the human antibody. The humanized antibody is useful as an effective component in a therapeutic agent according to the present invention since antigenicity of the humanized antibody in human body is lowered.
The antibody used in the present invention may be a fragment of the antibody or a modified fragment thereof, including divalent and monovalent antibodies. For example, the fragment of the antibody includes Fab, F(ab′)2, Fv, Fab/c having one Fab and a full Fc, and a single chain Fv (scFv) which is prepaerd by linking Fv of H chain and Fv of L chain via an appropriate linker. Specifically, an antibody is digested by an enzyme such as papain and pepsin to give the fragment of the antibody. Alternatively, genes encoding the above fragment are constructed and introduced into an expression vector, followed by the expression in a suitable host cell (Co, M. S. et al., J. Immunol. (1994) 152, 2968-2976, Better, M. & Horwitz, A. H. Methods in Enzymology (1989) 178, 476-496, Academic Press, Inc., Plueckthun, A. & Skerra, A. Methods in Enzymology (1989) 178, 476-496, Academic Press, Inc., Lamoyi, E., Methods in Enzymology (1989) 121, 652-663, Rousseaux, J. et al., Methods in Enzymology (1989) 121, 663-669, Bird, R. E. et al., TIBTECH (1991) 9, 132-137).
The scFv is prepared by linking Fv of H chain and Fv of L chain via an appropriate linker, preferably a peptide linker (Huston, J. S. et al., Proc. Natl. Acad. Sci. U.S.A. (1988) 85, 5879-5883). Each Fv of H chain and L chain may be derived from any antibody described in the present specification. The peptide linker used in the linking of V regions includes any single chain peptide having 12-19 amino acids.
A DNA encoding scFV may be prepared with the use of PCR in which amplification is done in the first step by using as template a DNA encoding all or a desired part of the amino acids in H chain or its V region and L chain or its V region and primers defining their both ends, and in the second step by using further a DNA encoding the peptide linker part and a pair of primers designed to ligate each end of the DNA with H chain and L chain, respectively.
Once the DNA encoding scFV is prepared, an expression vector comprising the DNA and a host cell transformed with the vector may be obtained according to a conventional method. The scFV may be produced with the use of the host cell by a conventional method as well.
The DNA encoding the above fragments of the antibody may be obtained, and these fragments of antibody may be expressed by the host cell as well. The “antibody” in the present invention includes these fragments.
As the modified antibody there may be mentioned those coupled with various molecules such as PEG. The antibody may be coupled with a radio isotope, a chemotherapeutic agent, a cytotoxic substance such as a bacteria toxin as well. The “antibody” in the present invention includes also these modified antibodies. These modified antibodies may be prepared by chemically modifying the resulting antibody by a conventional method.
The antibody used in the present invention also includes a bispecific antibody. The bispecific antibody may be the one having antigen-binding sites each of which recognizes a different epitope on the present protein, or the one having antigen-binding sites one of which recognizes an epitope on the present protein, and the other of which recognizes the chemotherapeutic agent or the cytotoxic substance such as a bacteria toxin. In the latter case, it is possible to directly apply the cytotoxic substance to a cell expressing the present protein (cancer cells) so that the cancer cells shall be specifically damaged and inhibited from growing. The bispecific antibody may be prepared by ligating a HL pair of two kinds of antibodies with each other, or by fusing hybridomas producing different monoclonal antibodies to give a hybridoma producing the bispecific antibody. Furthermore, the bispecific antibody may be prepared by genetic engineering technique.
The gene encoding the present antibody may be expressed and obtained by a known method. Where the mammalian cell is used, a conventionally used promoter, a gene for the antibody to be expressed and poly A signal 3′-downstream of the gene are functionally combined to express the gene. As a promoter/enhancer there may be mentioned human cytomegalovirus immediate early promoter/enhancer.
The other promoter/enhancers to be used in the present invention include promoter/enhancers derived from virus such as retrovirus, polyomavirus, adenovirus, and simian virus40 (SV40); and mammalian promoter/enhancer such as human elongation factor 1α (HEF1α).
SV40 promoter/enhancer and HEF1α promoter/enhancer may be used according to Mulligen, Nature (1979) 277, 108 and Mizushima et al., Nucleic Acids Res. (1990) 18, 5322, respectively, in order to easily express the gene.
A replication origin may be derived from SV40, polyoma virus, adenovirus, bovine papilloma vuirs (BPV), etc. The expression vector may further comprise a selection marker such as aminoglycoside transferase (APH) gene, thymidine kinase (TK) gene, E. coli xanthineguanine phosphoribosyl transferase (Ecogpt) gene, and dihydrofolic acid reductase (dhfr) in order to increase the number of copies of the gene in the host cell.
Where the E.coli is used, a conventionally used promoter, a signal sequence for secretion and a gene for the antibody to be expressed are functionally combined to express the gene. As a promoter/enhancer there may be mentioned lacz promoter and araB promoter, which are used according to Ward, Nature (1980) 341, 544-546; FASEB J. (1992) 6, 2422-2427, and Better, Science (1988) 240, 1041-1043, respectively.
A pelb signal sequence (Lei, S. P. et al., Bacteriol. (1987) 169, 4379) may be used for the production of the antibody in periplasma of E. coli. The antibody produced in the periplasma is separated and appropriately refolded for use.
The present antibody may be produced by any expression system such as eukaryotic and prokaryotic cell expression systems. The eukaryotic cell line includes established cells such as a mammalian cell, an insect cell, filamentous fungus, and yeast. The prokaryotic cell line includes bacteria cells such as E. coli. The antibody used in the present invention is preferably expressed in CHO, COS, myeloma, BHK, Vero, and Hela cells.
The transformed host cell is cultured in vitro or in vivo by a known method to produce the desired antibody. The culture medium includes DMEM, MEM, RPMI1640 and IMDM, which may be supplemented with a serum-supplementing agent such as fetal calf serum (FCS).
The thus expressed and produced antibody may be separated from the cell or host animal and purified to homogeneity. The separation and purification of the present antibody may be carried out with the use of an affinity column including Protein A column such as Hyper D, POROS, Sepharose F. F. (Pharmacia Co., etc.). Any other separation and purification methods which are used for usual proteins may be used. For example, the present antibody may be separated and purified with the use of a chromatography column other than the above affinity column, filter, ultra filtration, salting-out and dialysis, and any combination thereof (Antibodies A Laboratory Manual, Ed Harlow, David Lane, Cold Spring Harbor Laboratory, 1988).
Antigen-binding activity (Antibodies A Laboratory Manual, Ed Harlow, David Lane, Cold Spring Harbor Laboratory, 1988) and ligand receptor binding-inhibiting activity (Harada, A. et al., International Immunology (1993) 5, 681-690) may be determined by known methods.
The antigen-binding activity of the present antibody may be determined by ELISA (Enzyme Linked Immuno Sorbent Assay), EIA (Enzyme Immuno Assay), RIA (Radio Immuno Assay) and fluorescence antibody method. In the case of EIA, a sample containing the present antibody such as a culture supernatant of the cell producing the present antibody or a purified antibody is added to a plate coated with the present protein. After addition of a second antibody labeled with an enzyme such as alkaline phosphatase, the plate is incubated and washed. An enzyme substrate such as p-nitorophenyl phosphate is then added to the plate and absorbance is determined in order to evaluate the antigen-binding activity.
The present antibody may also have cytotoxicity activity such as complement-dependent cytotoxicity (CDC) activity and antibody-dependent cell-mediated cytotoxicity (ADCC) activity. The CDC activity in the present specification means cytotoxicity caused by a complement system, and the ADCC activity in the present specification means cytotoxicity caused by a cell having Fcγ receptor (e.g., immunocyte) which binds through its Fcγ receptor to the Fc portion of a specific antibody attached to a target cell.
The presence of CDC or ADCC activity of the present antibody may be determined by a known method (e.g., Current protocols in Immunology, Chapter 7. Immunologic studies in humans, Editor, John E., Coligan et al., John Wiley & Sons, Inc., (1993)).
Specifically, the cytotoxicity activity may be determined as follows:
Preparation of Effecter Cells
Spleen is extracted from CBA/N mouse and the like, and spleen cells are separated in RPMI1640 culture medium (GIBCO Co.). The cells are washed in the same medium containing 10% FBS (Hyclone Co.) and concentration of the cells is adjusted to 5×106/ml to give an effecter cell preparation.
Preparation of a Complement Solution
A complement solution is prepared by diluting Baby Rabbit Complement (CEDARLANE Co.,) ten times with the above medium containing 10% FBS (Hyclone Co.).
Preparation of Target Cells
The cells expressing the present protein (prostatic adenocarcinoma, ovarian carcinoma, colon adenocarcinoma, etc) are incubated with 0.2 mCi 51Cr-sodium chromate (Amersham Pharmacia Biotech Co.) in DMEM medium containing 10% FBS for one hour at 37° C. so as to be labeled with a radioisotope. After labeling with the radio isotope, the cells are washed three times with RPMI1640 medium containing 10% FBS and concentration of the cells is adjusted to 2×105/ml to give a target cell.
Determination of ADCC Activity
The present antibody (50 μl) and the target cell (50 μl) are added into a 96 U-well plate (Beckton Dickinson Co.) and reacted for 15 min. on ice. The effecter cell (100 μl) is then added and the resulting mixture is cultured for 4 hours in CO2 incubator. The final concentration of the antibody is adjusted to 0 or 10 μg/ml. After the completion of the culture, 100 μl of supernatant is recovered and subjected to the determination of radioactivity by means of a gamma counter (COBRAIIAUTO-GMMA, MODEL D5005, Packard Instrument Company). The cytotoxicity (%) is calculated based on the formula: (A−C)/(B−C)×100 wherein “A” is the radio activity (cpm) of each test sample, “B” is the radio activity (cpm) of a sample mixed with 1% NP-40 (Nakarai Ltd.), and “C” is the radio activity (cpm) of a sample containing only the target cell.
Determination of CDC Activity
The present antibody (50 μl) and the target cell (50 μl) are added into a 96 U-well plate (Beckton Dickinson Co.) and reacted for 15 min. on ice. The complement solution (100 μl) is then added and the resulting mixture is cultured for 4 hours in CO2 incubator. The final concentration of the antibody is adjusted to 0 or 3 μg/ml. After the completion of the culture, 100 μl of supernatant is recovered and subjected to the determination of radioactivity by means of the gamma counter. The cyototoxicity is determined by the same way as in ADCC activity.
[Anti-Cancer Agent According to the Present Invention]
An effective amount of administration of the anti-cancer agent of the present invention usually ranges from 0.00 mg ̃1,000 mg per 1 kg weight, or 0.01 ̃100,000 mg/body of patient, being, however, not limited to these ranges. The present agent may be administered before or after the occurrence of clinical symptom. The present agent may be prepared according to a known method (Remington's Pharmaceutical Science, latest edition, Mark Publishing Company, Easton USA), while being optionally mixed together with pharmaceutically acceptable carriers or additives. These pharmaceutically acceptable carriers or additives include, for example, water, pharmaceutically acceptable organic solvent, collagen, polyvinylalcohol, polyvinylpyrrolidone, carboxylvinylpolymer, sodium carboxylmethylcellulose, sodium polyacrylate, sodium alginate, aqueous dextran, sodium carboxylmehylstarch, pectin, methylcellulose, ethylcellulose, xanthan gum, arabic gum, casein, agaraose, polyethylenglycol, diglycerine, glycerine, propylene glycol, petroleum jelly, paraffin, stearic alcohol, stearic acid, human serum albumin (HSA), mannitol, sorbitol, lactose, and pharmaceutically acceptable surfactant. The carries or additives may be optionally selected from the above-listed substances depending on a formulation type of the present agent. A preparation for injection may be a solution in solvent such as physiological saline, buffer solution and glucose solution supplemented with absorption-inhibiting agent such as Tween80, Tween20, gelatin, and HSA. A preparation of the present agent may be lyophilized and dissolved before use, including sugars or sugar alcohols such as mannitol and glucose as an excipient for lyophilization. The present agent is usually administered parentally, for example, by injection (subcutaneously, intravenouly, intramuscularly, intraperitoneally, etc.), percutaneously, permucously, administration through nose or lung, but may be administered orally as well.
[Method of Screening a Substance which Binds to the Above Protein or a Partial Peptide thereof]
The present protein is useful in screening of a substance which binds to it. Thus, it is used in a method of screening a substance which binds to the present protein, which comprises bringing a sample seemingly containing the substance in contact with said protein, detecting a binding activity between the sample and said protein and selecting a substance which has the binding activity.
The present protein used in the screening method may be a recombinant one, naturally occurring one, or a partial peptide thereof. Any material may be used as a sample of the method, including, for example, cell extracts, cell culture supernatants, products by fermenting bacteria, extracts from marine organisms, plant extracts, (crudely) purified proteins, peptides, non-peptide compounds, synthetic low molecular compounds, and natural compounds. The present protein to be brought in contact with the sample may be used as a purified one, a solubilized one, a complex with a carrier, a fused one with other proteins, an expressed one on a cell membrane, or a membrane component.
For example, a protein such as a ligand binding to the present protein may be screened with the use of any method known for those skilled in the art. These methods include Immunoprecipitation (Harlow, E. and Lane, D.: Antibodies, pp. 511-552, Cold Spring Harbor Laboratory publications, New York (1988)), West-Western blotting (Skolnik, E. Y. et al., Cell (1991) 65, 83-90), Two-hybrid system using cells (Fields, S., and Sternglantz, R., Trend. Genet. (1994) 10, 286-292, Dalton S, and Treisman R., (1992) Characterization of SAP-1, a protein recruited by serum response factor to the c-fos serum response element, Cell, 68, 597-612, [MATCHMAKER Two-Hybrid System][Mammalian MATCHMAKER Two-Hybrid Assay Kit][MATCHMAKER One-Hybrid System] (Clontech Co.), [HybriZAP Two-Hybrid Vector System] (Stratagene Co.), Affinitiy chromatography, and biosensor using surface plasmon resonance phenomenon.
The method for the separation of the compounds including protein, which bind to the present protein, includes known methods such as a screening method wherein the fixed present protein is reacted with a synthesized compound, a bank of natural materilas, and a random phage display library, and a molecular which can bind to the present protein is selected; and a screening method wherein a high through-put reaction is done by means of combinatorial chemistry technique (Wrighton N C; Farrell F X; Chang R; Kashyap A K; Barbone F P; Mulcahy L S; Johnson D L; Barrett R W; Jolliffe L K; Dower W J; Small peptides as potent mimetics of the protein hormone erythropoietin, Science (UNITED STATES) Jul. 26, 1996, 273 p458-464, Verdine G L., The combinatorial chemistry of nature, Nature (ENGLAND) Nov. 7, 1996, 384 p 11-13, Hogan J C Jr., Directed combinatorial chemistry, Nature (ENGLAND) Nov. 7, 1996, 384 p 17-17).
Since the compound which can be separated by the screening method according to the present invention may be a substance which inhibits the binding between the present protein and ligand, it will be utilized in an anti-cancer agent. Thus, the anti-cancer agent may be prepared by combining the compound separated by the present screening method with pharmaceutically acceptable carries.
[Others]
An antisense oligonucleotide (DNA) having a nucleotide sequence substantially complementary to a DNA encoding the present protein or a partial polypeptide thereof includes any antisense DNA as long as it has a nucleotide sequence substantially complementary to said DNA and has a function to inhibit the expression of the same DNA. The “nucleotide sequence substantially complementary” means, for example, that it has homology preferably of about 90% or more, more preferably of about 95% or more, most preferably of 100% to the whole or partial sequence of a nucleotide sequence complementary to the present DNA. Any nucleic acid sequence (a modified DNA or RNA) which shows a function similar to that of the antisense DNA is also included in the antisense DNA according to the present invention. These antisense DNAs may be prepared with a known DNA synthesizer.
The present DNA or gene comprising thereof may be used as a probe to detect abnormality in the DNA or its mRNA (genetic abnormality) encoding the present polypeptide or its partial peptide. They are therefore useful as a genetic diagnosis agent for detecting damage, mutation and under-expression of the DNA or mRNA; or for detecting increase and over-expression of the DNA or mRNA. The genetic diagnosis with use of the present DNA may be done by a known method such as Northern hybridization and PCR-SSCP (Genomics vol. 5, 874-879 (1989), Proceedings of the National Academy of Science of the United States of America, vol. 86, 2766-2770 (1989)).
The function of the protein according to the present invention can be effected in a patient in whom the present DNA or gene dose not normally function due to its abnormality, deletion or under-expression by a known method such as (1) the one in which the present DNA or gene is introduced into the patient and expressed by gene therapy with the use of an appropriate vector such as retrovirus vector, adenovirus vector and adenovirus-associated virus vector; and (2) the one in which they are injected into the patient.
The present DNA or gene may be also administered alone or in combination with an auxiliary to promote uptake by means of a gene gun or a catheter such as a hydrocatheter.
Single mutation in the present DNA or gene (cSNP), which is different from each individual, may be found by doing PCR of a chromosomal DNA extracted from human blood or tissue with the use of a synthetic DNA primer prepared based on the whole or partial nucleotide sequence of the present DNA or gene, and determining the nucleotide sequence of the PCR products. Individual constitution may be predicted by such cSNP, making possible to develop a drug suitable for each person.
Causal or responsible genes for human disorders may be searched and detected by isolating an orthologue (homologue or counterpart)) gene corresponding to the present DNA or gene in a model animal such as mouse, and making a model animal of the disorders with the use of knock out technique.
The abbreviation for a base and amino acid is shown in the present specification in accordance with IUPAC-IUB Commision on Biochemical Nomencalture or conventional methods, and an optical isomer of the amino acid, if any, means its L-isomer unless otherwise instructed.
EXAMPLES
The present invention will by further explained by the following examples, which do not limit the scope of the present invention. The genetic procedures in the examples are done in accordance with those described in Current protocols in molecular biology (edited by Frederick M. Ausubel et al., 1987).
(1) Construction of cDNA Library Derived from Human Adult Whole Brain, Human Amygdala, Human Adult Hippocampus, and Human Fetal Whole Brain
A double-stranded cDNA was synthesized by SuperScriptII reverse transcriptase kit (Invitrogen Co.) with the use of an oligonucleotide having NotI site (GACTAGTTCTAGATCGCGAGCGGCCGCCC(T)15) (SEQ ID NO: 3) (Invitrogen Co.) as a primer, and mRNA derived from human adult whole brain, human amygdala, human adult hippocampus, and human fetal whole brain (Clontech Co.) as a template. An adapter having SalI site (Invitrogen Co.) was ligated with the resulting cDNAs. After digestion with NotI, the cDNAs were subjected to electrophoresis on a low-melting agarose of 1% to purify cDNA fragments with 3 kb or more.
The thus purified cDNA fragments were ligated with pBluescript II SK+plasmid treated with SalI-NotI restriction enzymes. The resulting recombinant plasmids were introduced into E.coli DH10B strain (Invitrogen Co.) by an electroporation method.
(2) Screening (No. 1)
Clones were randomly picked up from the thus constructed cDNA library and spotted on a membrane. A mixture of oligoDNAs (21 base-long each) prepared on the basis of the nucleotide sequences of about 1,300 clones which had been analyzed about their whole nucleotide sequences were labeled with DIG by terminal transferase at their 3′-ends. Overlapping clones which will appear repeatedly were then removed by dot hybridization with use of the mixture of the above labeled oligoDNAs as a probe (Current protocols in molecular biology (edited by Frederick M. Ausubel et al., 1987).
After the transcription and translation system in vitro (Promega Co., TNT T7 Quick Coupled Transcription/Translation System cat. no. L1107), clones expressing products with 50 kDa or more were selected.
The terminal nucleotide sequences of the selected clones were determined, and the homology search was done on nr database (all GenBank+EMBL+DDBJ+PDB sequences, but no EST, STS, GSS or phase 0.1 or 2 HTGS seqeunces) with the use of the resulting sequences as a query in accordance with homology search program BLASTN2.2.1 (Altshul, Stephen F., Thomas L. Madden, Alejandro A., Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), “Gapped BLAST and PSI-BLAST: a new generation of protein search programs.”, Nucleic acids Res. 25:3389-3402). As a result, a gene having no homologous gene, i.e., a novel gene, is subjected to the whole nucleotide sequence analysis.
Screening (No. 2)
The terminal sequences of 3′- and 5 ′-ends of the above cDNAs were aligned with human genomic sequence (ncbi.nlm.nih.gov/genomes/H—sapiens/) with the use of homology search program BLASTN2.2.1.
Genes were picked up from a genome region inserted between them by the use of Genscan program (computer software for predicting a gene from genome sequences) (Burge, C. and Karlin, S. 1987, Prediction of complete gene structures in human genomic DNA, J. Mol. Biol., 268, 78-94). Homology search was done on mergedb, which had been prepared by combining human cDNA sequences determined by KAZUSA DNA Institute and Homo sapiens database of GenBank (except EST and genome) without overlapping data, with the use of the selected genes as a query in accordance with homology search program BLASTN2.1.3. When a novel long-ORF gene (with 1,200 bp or more of cds according to the prediction by Genscan) was found, the full-length sequences of its 5′- and 3′-ends were determined.
Determination of the nucleotide sequence was carried out by means of a DNA sequencer (ABI PRISM377) and a reaction kit manufactured by PE Applied Bio System Co. Most of the sequences were determined by a diterminator method on shotgun clones, and parts of them were determined by a primer-walking method with the use of oligonucleotides that were synthesized based on the thus determined nucleotide sequences.
The novel DNAs or genes were screened in the above ways. As a result, a done pj01304 was found. Furthermore, the 3′- and 5′-end sequences of about 100,000 clones isolated from brain cDNA library prepared by Ohara et al. and about 2,000 full-length clones were assembled together, and grouping of cDNA clones derived from the same gene was done.
As a result, a clone pj05443 comprising an upstream region of the clone pj01304 was finally found in a group containing the clone pj01304.
The upstream region of the clone pj01304 was then excised from the clone pj05443 and ligated with the clone pj01304 to give a clone pj01304s1 (KIAA1742) comprising the novel DNA or gene represented in SEQ ID NO. 1 or NO. 2 according to the present invention. The nucleotide sequence from 1 bp to 820 bp of the clone pj01304s1 is derived from the clone hj05443, and that from 821 bp to 5,035 bp is derived from the clone pj01304.
(3) Expression of the Protein Encoded by the Present Gene
A gene product was expressed from the cDNA clone pj01304 with the use of the transcription and translation system in vitro (Promega Co., TNT T7 Quick Coupled Transcription/Translation System cat. no. L1107).
The product incorporated with 35S-labeled methionine was subjected to SDS-PAGE (12.5%). After drying of a gel, autoradiography was done with the use of BAS2000 (Fuji film) system to detect the gene product of the clone pj01304. As a result, a band, which was presumed to be a transcription/translation product of the done pj01304, was observed at a point corresponding to a marker with 135 kDa.
As a molecular weight of the protein encoded by the pj01304 consisting of 1,137 amino acids from a first methionine is presumed to be about 124 kDa, the presumed molecular weight was coincided well with the above result.
(4) Homology Research of the Present DNA
The homology search of the whole nucleotide sequence thus determined was done on the known nr data in accordance with homology search program BLASTN2.2.1 (Altshul, Stephen F., Thomas L. Madden, Alejandro A., Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), “Gapped BLAST and PSI-BLAST: a new generation of protein search programs.”, Nucleic acids Res. 25:3389-3402). As a result, the present DNA has homology to a gene shown in Table 1. Table 1 shows information about the gene (homologous gene) such as its name, data base ID, species, length of protein, etc. The meaning of each item in Table 1 is as follows:
“Homologous region, clone”: the starting and ending points of the homologous region in the present clone;
“Homologous region, homologous gene”: the starting and ending points of the homologous region in the homologous gene;
“Score”: the higher this value is, the higher credibility is;
“E-value”: the closer this value comes to “0”, the higher credibility become;
“Homology”: the percentage of identical amino acids in the homologous region; and
“Percentage of the homology region”: the percentage of the homologous region in the homologous gene.









TABLE 1









Homology Value











Homologous region



Percentage













Homologus



of the


Clone
gene



homology














from
to
from
to
Score
E-value
Homology
region





59
913
236
1125
423
e−117
31%(287/923)
73%










Homologous gene











Name
Data base
Species
Length of protein
Publication





CG2019
gblAAF51938.1l
Dm
1218
—









(5) Search of Domains

The DNA according to the present invention (KIAA1742) is a gene with 5,035 bp encoding a protein with 1,245 amino acids. Motif search by the use of HMMER2.1.1 (S. R. Eddy. Profile hidden Markov models. Bioinfomatics 14:755-763, 1998) revealed the existence of a motif of Patched family which is involved in a signal of hedgehog-smoothend in the region of amino acids No. 145-954.
Further, the search with the use of Sosui (Bioinformatics (1998) May; 14(4):378-379) predicted the presence of 12 transmembrane regions as shown in Table2. It was assumed that the region of amino acids No. 39-328 (a region between the first and second transmembrane regions) and the region of amino acids No. 560-802 (a region between the seventh and eighth transmembrane regions) constituted a large loop, which was very similar to the structure of Patched (Cell 59, 751(1989); Cancer Letter (2001) 173, 1-7) as shown in FIG. 1.
TABLE 2; SEQ ID NOS: 6-17, in order from top to bottom, respectively.











TABLE 2





No
N terminal
transmembrane region
C terminal
length




















1
14
VAVLMLCLAVIFLCTLAGLLGARLP
38
25



 


2
329
LVQDTVYPLLALVAIFFGMALYLRS
353
25


 


3
357
TLMVLLGVLGSLLVAFFLYQVAFRM
381
25


 


4
385
PFVNLAALLLLSSVCANHTLIFFDL
409
25


 


5
433
FGYLLLVSGLTTSAAFYASYLSRLP
457
25


 


6
463
ALFMGTAVLVHLALTLVWLPASAVL
487
25


 


7
535
FQRLLPCGVIKFRYIWICWFAALAA
559
25


 


8
803
SLSTEPAVVLGLALALAFATLLLGT
827
25


 


9
831
PLSLFSVAAVAGTVLLTVGLLVLLE
855
25


 


10
864
LFLSASVGLSVDFTVNYCISYHLCP
888
25


 


11
902
QTSCATAVGAAALFAAGVLMLPATV
926
25


 


12
934
IILMMVKCVSCGFASFFFQSLCCFF
958
25









Brief Explanation of Table 2
The amino acid sequences and locations of the predicted 12 transmembrane regions are shown in Table 2. “N terminal” and “C-terminal” show the number of the amino acid at N-terminal and C-terminal, respectively. “Length” means the length of transmembrane region.
“Patched” was found in Drosophia as a protein having 12 transmembrane regions, which functions as a tumor suppressor of blocking a signal of Smoothend. Patched has two large hydrophllic and extracellular loops, and transmits the signal through direct or indirect interaction with Smoothend. However, it is assumed that the binding of Hedgehog will release the blocking of the signal of Smoothend and cause basal cell carcinoma. Patched is known to control the transcription of members of TGFβ such as BMP or Wnt families (EMBO J (1998) 17, 3505-3511), Cancer Letter (2001) 173, 1-7). It has been reported that Hptc (Human gene homologue to ptc) is involved in skin carcinoma (Am J Pathol (2001) 158, 381-385, PNAS (1999) 96, 5117-5122).
The present protein belonging to Patched family has homology of 31% to Dispatched of the same family, and it is the protein having 12 transmembrane regions like Patched. Gene expression profiling showed that increase of the expression of the present gene was observed in prostatic adenocarcinoma and ovarian carcinoma in, it is assumed that the present gene acts as an oncogene, but not as a tumor suppressor gene like Patched. It is conceived that the present protein will interact with Smoothend or other proteins through the two large extracellular loops and transmit cancer signal. Or it may competitively act against the binding between Hedgehog and Patched, and transmit cancer signal.
In view of the above knowledge and information about the biological activity (function) of the present DNA, it is considered that the present DNA is a cancer-associated gene, and that it is possible to inhibit cancer by blocking the binding of the present protein to its ligand.
Accordingly, the present antibody is used not only in the detection of the present protein, but also as an agent for the treatment or prevention of cancers such as prostatic adenocarcinoma and ovarian carcinoma
(6) Real-Time PCR Analysis of the Transcription Products
An amount of the transcription product of the present gene were analyzed by using cDNA in each tissue with ABI PRISM® 7700 Sequence Detection System (ABI Co.) The expression amount of GAPDH gene was analyzed with Pre-Developed TaqMan PCR Assay Kit (ABI Co. #4310884E). Master Mix was prepared by mixing 1.25 μl of 20×Control Mix (GAPDH), 6.25 μl of DEPC-treated water (Ambion Co. #9920) and 12.5 μl of TaqMan Universal PCR Master Mix (ABI Co. #4304437). After the addition of 5 μl of MTC Panel cDNA (Clontech Co.) to the Master Mix to a final volume of 25 μl, gene amplification was done by 2 min. at 50° C., 10 min. at 95° C., and repeating 40 cycles of 15 sec. at 95° C. and 1 min. at 60° C. on MicroAmp Optical 96-wel Reaction Plate (ABI Co. #N801-0560). Human MTCTM Panel I (K1420-1), Human MTCTM Panel II (K1421-1) and Tumor MTCTM Panel I (K1422-1) were used as MTC Panel cDNA.
An expression amount of the present gene was analyzed by amplification with the use of a primer 1742-3538 (5′-CAGCACTCACACGTCAGGCT-3′) (SEQ ID NO: 4), and a primer 1742-3658 (5′-AGAAATACCTTCGGGCTCCAG-3′) (SEQ ID NO: 5). O.5. of the primer 1742-3538 (10 μM), 0.5 μl of the primer 1742-3658 (10μM), 6.5μl of DEPC-treated water, 12.5 μl of SYBR Green PCR Master Mix (ABI Co. #4309155) were mixed together to a final volume of 20 μl, followed by the addition of 1 μl of MTC Panel cDNA (Clontech Co.) and 4 μl of DEPC-treated water to a final volume of 25 μl. Gene amplification was done by 2 min. at 50° C., 10 min. at 95° C., and repeating 40 cycles of 20sec. at 95° C., 30sec. at 59° C., and 30sec. at 72° C. on MicroAmp Optical 96-well Reaction Plate (ABI Co. #N801-0560) with the use of ABI PRISM® 7700 Sequence Detection System (ABI Co.). Relative values were calculated based on a standard curve of control cDNA attached to MTC Panel with the use of the expression amount of GAPDH gene GAPDHgene as a standard control. A vector comprising the present gene cloned in pBluescript (40 pg/μl) was serially diluted 5 times and the resulting solutions were then used as reference. The relative values in each tissue obtained by dividing the expression amount of the present gene by that of GAPDH gene are summarized and compared among one another in Table 3.
In Table 3, figures in the right column indicate the expression amount of the KIAA1742 gene, which was normalized with the expression amount of GAPDH gene in each tissue, and shown as a relative value against prostate of value “1”.
Table 3 clearly shows that the high values are obtained in prostatic adenocarcinoma and ovarian carcinoma.










TABLE 3







Tissue
KIAA1742/GAPDH



















Heart
0.28



Brain
36.60



Placenta
1.97



Lung
1.78



Liver
3.85



skeletal muscle
0.06



Kidney
0.57



Pancreas
3.60



Spleen
2.57



Thymus
0.48



Prostate
1.00



Testis
5.87



Ovary
1.10



small intestine
6.81



Colon
13.03



peripheral blood leukocyte
0.27



breast carcinoma GI-101
0.61



lung carcinoma LX-1
0.46



colon adenocarcinoma CX-1
8.87



lung carcinoma GI-117
0.12



prostatic adenocarcinoma PC3
229.78



colon adenocarcinoma GI-112
0.99



ovarian carcinoma
28.36



pancreatic adenocarcinoma GI-103
0.87










(7) Location on Chromosome

It was further confirmed that the present gene was expressed in cerebellum with the use of PT-PCR Coupled ELISA. Alignment of the DNA sequence of the present clone with a human genomic library (ncbi.nlm.nih.gov/genomes/H—sapiens/) showed that the present gene was located on chromosome 15.
(8) Preparation of pj01304s1(KIAA1742) Gene Family
Homology search of the DNA sequence of the pj01034s1 gene was done on human genomic sequences (ftp://ncbi.nlm.nih. gov/genomes/H—sapiens/) in accordance with BLSTN2.2.1 hit a particular genomic fragment (GenBank ID NT—010194.6).
The pj01304GS gene, which has a high homology to the pj01304s1 gene (100% at DNA level and 100% at protein level; aligned by GenWorks (Intelligenetics Co.)), was then found with the use of Genscan program (Burge, C. and Karlin, S. 1987, Prediction of complete gene structures in human genomic DNA, J. Mol. Biol., 268, 78-94: computer software for predicting a gene from genome sequences). The pj01304GS gene has 4,479 bp, which encodes a protein having 1,492 amino acids. Its nucleotide sequence and amino acid sequence are shown as SEQ ID NO. 2.
The alignment between the pj01304GS gene and the pj01304s1 gene is shown in Table 4. As seen from Table 4, an amino acid sequence of No. 248-1,492 encoded by the pj01304GS gene is identical with an amino acid sequence of No. 1-1,245 encoded by the pj01304s1 gene, showing that the pj01304GS gene has a nucleotide sequence encoding an amino acid sequence of No. 1-247 located 5′ upstream of the pj01304s1 gene. Accordingly, it is considered that both the genes are generated from the same genome by an alternative splicing. It is also considered that as the pj01304GS gene has the same domains as the pj01304s1 gene, it will show similar activities. Thus, the pj01304GS gene and protein encoded thereby are included in the DNA and protein according to the present invention, respectively.
Those skilled in the art may easily prepare those genes by, for example, RT-PCR. Thus, PCR is done by the use of an upstream primer (5′-ATGGGAAGAAAGACCCAACC-3′: 1 ̃20 bp of the SEQ ID NO. 2) and a downstream primer (5′-CAAGTCCTGGCAGGGAACTG-3′: 588 ̃607 bp of the SEQ ID NO. 2), and cDNA as a template obtained by reverse transcription from human adult cerebellum mRNA with random primers. The resulting DNA is then ligated with the pj01304s1 gene by known methods such as Chuan Li et al., Ligation independent cloning irrespective of restriction site compatibility, Nucleic Acids Res. 1997 25:20 (4165-4166) to give a clone encoding the pj01304GS protein.
Alignment of pj0130405 (SEQ ID. NO:2) with pj01304s1 (SEQ ID NO:1) showing consensus sequence (SEQ ID NO:2).









TABLE 4







pj01304GSpj01304s1Consensus




50 50


 


pj01304GSpj01304s1Consensus




100 100


 


pj01304GSpj01304s1Consensus




150 150


 


pj01304GSpj01304s1Consensus




200 200


 


pj01304GSpj01304s1Consensus




250 3250


 


pj01304GSpj01304s1Consensus




300 53300


 


pj01304GSpj01304s1Consensus




350103350


 


pj01304GSpj01304s1Consensus




400153400


 


pj01304GSpj01304s1Consensus




450203450


 


pj01304GSpj01304s1Consensus




500253500


 


pj01304GSpj01304s1Consensus




550303550


 


pj01304GSpj01304s1Consensus




600353600


 


pj01304GSpj01304s1Consensus




650403650


 


pj01304GSpj01304s1Consensus




700453700


 


pj01304GSpj01304s1Consensus




750503750


 


pj01304GSpj01304s1Consensus




800553800


 


pj01304GSpj01304s1Consensus




850603850


 


pj01304GSpj01304s1Consensus




900653900


 


pj01304GSpj01304s1Consensus




950703950


 


pj01304GSpj01304s1Consensus




1000 7531000


 


pj01304GSpj01304s1Consensus




1050 8031050


 


pj01304GSpj01304s1Consensus




1100 8531100


 


pj01304GSpj01304s1Consensus




1150 9031150


 


pj01304GSpj01304s1Consensus




1200 9531200


 


pj01304GSpj01304s1Consensus




125010031250


 


pj01304GSpj01304s1Consensus




130010531300


 


pj01304GSpj01304s1Consensus




135011031350


 


pj01304GSpj01304s1Consensus




140011531400


 


pj01304GSpj01304s1Consensus




145012031450


 


pj01304GSpj01304s1Consensus




149212451492









INDUSTRIAL APPLICABILITY 
In view of the above knowledge and information, it is considered that the present DNA is a cancer-associated gene, and that it is possible to inhibit cancer by blocking the binding of the present protein to its ligand.
Accordingly, the present antibody is used not only in the detection of the present protein, but also as an agent for the treatment or prevention of cancers such as prostatic adenocarcinoma and ovarian carcinoma

## Claims

1. An isolated DNA consisting of the nucleotide sequence encoding
the polypeptide consisting of the amino acid sequence of SEQ ID NO: 18.

2. An isolated DNA consisting of the nucleotide sequence of SEQ ID NO:1 or the nucleotide sequence consisting of nucleotides 561-4295 of SEQ ID NO: 1.

3. An isolated gene comprising the DNA of claim 1 or claim 2.

4. An expression vector comprising the isolated DNA of claim 1 or 2 or an isolated gene comprising the DNA of claim 1 or claim 2.

5. A isolated transformant transformed with the expression vector of claim 4.

6. A method for the expression of an isolated DNA comprising culturing the transformant of claim 5.

7. A method for the production of a protein, comprising:
culturing the transformant of claim 5, and
recovering the protein expressed from said transformant or the culture supernatant thereof, wherein the protein is encoded by the nucleotide consisting of nucleotides 561-4295 of SEQ ID NO: 1.