EP1037986A1 - Gene associated with neoplastic disease or malignancy associated gene - Google Patents

Abstract

A nucleic acid encodes a polypeptide associated with liver neoplastic diseases, such as liver cirrhosis and hepatocellular carcinoma, among others. Significantly, the polypeptide is not expressed in normal, non-neoplastic liver. An antibody(ies) binds to the polypeptide of the invention. The polynucleotide, polypeptide and antibody are also provided in kits, and applied to the diagnosis of, and screening of populations for, neoplastic diseases such as liver disease.

Description

GENE ASSOCIATED WITH NEOPLASTIC DISEASE OR MALIGNANCY ASSOCIATED GENE

BACKGROUND OF THE INVENTION

This application is a continuation-in-part of United States Patent Application Serial No. 08/989,750, entitled "Gene Associated with Liver Neoplastic Disease or Malignancy Associated Gene", filed December 12, 1997, which is a continuation-in-part of United States Patent Application Serial No. 08/533,996, entitled "A Gene Associated with Liver Neoplastic Disease", filed September 27, 1995, by the same inventors.

This invention was made at least partially under the sponsorship of United States Government support under Grant No. DK38763-10 (AAD) from the National Institutes of Health. The United States Government may have rights in this invention.

Field of the Invention

The present invention relates to a gene that encodes a protein associated with neoplastic liver diseases, such as liver cirrhosis and hepatocellular carcinoma. The protein encoded by the gene of this invention has not been found to be expressed in normal, non-neoplastic liver tissue. The present invention also relates to a diagnostic method or assay and a .kit suitable for assessing a subject's neoplastic status as well as for screening of a population for liver neoplastic disease. Description of the Background

Hepatocellular carcinoma (HCC) is reported to afflict as many as 260,000 individuals each year world- wide, malting it the eighth most frequent cancer in the world. Cirrhosis has been implicated as a predisposing condition for HCC in a majority of patients who develop HCC in low risk populations. Approximately 80-90% HCC cases have been found to occur in patients suffering from cirrhotic liver.

Current therapies for liver cirrhosis include treatment with corticosteroids and interferon- . However, in more severe cases, a liver transplant is often the only recourse, Although the disease reocurs in a year or earlier. Similarly, treatment for benign and malignant liver tumors is often either a liver resection or a liver transplant. These more drastic treatments are both very risky and very expensive. Thus, early diagnosis and treatment of liver neoplastic diseases, such as liver cirrhosis and HCC, is highly desirable. It has been reported that α-fetoprotein and IGF-II are expressed in the liver tissue of approximately 30% of those individuals afflicted with HCC, but not in normal adult liver. Unfortunately, these proteins appear more frequently in late stage HCC and thus, are not suitable for the development of an early diagnostic test. Efforts to develop methods for diagnosis and treatment have been slowed by the lack of understanding of the pathology of HCC. In spite of the clinical importance of liver cirrhosis and HCC, the mechanism of HCC development still remains obscure. Tremendous gaps exist in the current understanding of basic pathologic mechanisms that lead to the development of HCC. Cellular protooncogenes, tumor suppressor genes (antioncogenes), and DNA mismatch repair mutations are generally considered as key molecular genetic biomarkers of carcinogenesis. However, only a few genes are more or less specific for particular neoplastic tissue and can be used as diagnostic factors to design effective treatment regimens. Concurrent loss of p53 and K-ras function may contribute to the clinical aggressiveness of pancreatic carcinomas, loss or mutation of a new candidate tumor suppressor, DPC4 (deleted in pancreatic carcinoma locus 4), has been reported in pancreatic cancer. In breast cancer, HER-2/neu amplification has greater prognostic value than most currently used prognostic factors). Overexpression of HER-2/neu rarely occurs in the absence of gene amplification in breast cancer (approximately 3% of cases). Prostate specific antigen (PSA) expression is a marker for prostate cancer. In liver cancer, (α-fetoprotein, an embryonic protein, is expressed in 26-53 % of cases basically at the late stages of cancer development. Insulin like growth factor II (IGF-II), a fetal growth factor, is overamplified in some cases of human hepatocellular carcinoma (HCC) and can be expressed in altered hepatic foci in woodchuck hepatitis virus carriers. In this report, a partial characterization and tissue expression is provided for a novel gene that is expressed only in advanced ciirhosis (late stage), premalignant (macroregenerative nodules with displasia of the liver), and malignant tissues but not in any of the normal tissues tested. It has been tentatively designated malignancy-associated gene, or MAG.

Accordingly, the identification of novel genetic markers associated with liver diseases, such as liver cirrhosis and HCC, is highly desirable, as is their application to the diagnosis and therapy which will be brought about by the further elucidation of the pathology of these diseases. SUMMARY OF THE INVENTION

The present invention relates to a protein which has been found to be unequivocally associated with neoplastic liver disease, such as liver cirrhosis and hepatocellular carcinoma, and to the gene that encodes it. This protein has not been found to be expressed in normal liver but it is expressed in fetal figures, malting the gene an oncofetal gene. The protein and DNA encoding it are also provided in the form of compositions and kits, and they are useful for the detection and diagnosis of subjects and for screening populations which may be afflicted with the associated diseases or malignancies.

The invention also relates to antibodies that bind to the polypeptide of the invention. These antibodies, monoclonal and polyclonal, are also provided in the form of a composition and kit, and are suitable for the assessment of the presence of malignant cells or molecular markers like proteins and nucleic acids or their fragments in a biological sample and, therefore, for diagnosis and screening of populations for neoplastic disease. This invention is, thus, useful in the diagnosis and prevention of neoplastic disease.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

This invention arose from a desire by the inventors to improve on prior art technology for the detection of cancer, including liver cancer, such as hepatocarcinoma, liver cirrhosis, and the like and, therefore, to facilitate the prevention and therapy of such diseases. Up to the present time, the diagnosis of various neoplastic diseases, particularly neoplastic liver disease, has been rather erratic. Therapy is generally implemented by administration of corticosteroids and interferon-α, and in more extreme cases by surgery and liver transplant. None of the available therapies are entirely satisfactory when applied at an advanced stage of the disease. The inventors, therefore, surmised that the availability of an efficient detection method would permit an early detection of neoplastic liver ailments and, thus, their treatment before more drastic actions are required. The present invention, therefore, relies on the finding by the inventors of a novel nucleic acid encoding a pep tide of up to about 104 amino acids long. This peptide was found to be characteristically expressed in individuals afflicted with neoplastic diseases, such as cirrhosis and hepatocellular carcinoma (HCC), and in fetal tissues, but not in individuals with normal, non-neoplastic liver function. Because of its direct association with malignancies the present gene was named Malignancy Associated Gene or MAG, and because it is also present in fetal atissue it is considered an oncofetal gene.

A stretch minus strand was found, which is located within a 54 kb genomic sequence outside of the human ERCC2 gene and of the two adjacent genes, C and KLC2, referred to as the "ERCC2 gene cluster". See, GenBank data base. The three-gene sequence was found in a centromeric direction between the KLC2 and CKMM genes, and to have 95% sequence homology with the present 569 bp DNA fragment. The 3'RACE-PCR work reported here yielded a continuous gene sequence from the initial fragment down to the poly (A) tail, evidencing the presence of mRNA for the gene. A control experiment by which RNA samples were pretreated with RNase-free DNase and DNase-free RNase before RT-PCR was conducted (data not shown) after DNase treatment of RNA samples a band of MAG gene was obtained, after RNase treatment no band was present. Thus, it is highly unlikely that the novel gene was aitifactually amplified from a residual DNA present as a contaminant in the RNA preparations. This possibility was further ruled out using the RPA described in the examples, which showed the presence of MAG mRNA in HepG2 liver tumor cell line and in ovarian cancer. The novel MAG gene was found to be absent from normal tissues but present in premalignant and malignant tissues. The expression of the MAG gene was detected not only in liver cirrhosis and premalignant macroregenerative nodules with displasia and HCC, but in other human malignancies such as lung, breast, spleen, .kidney, colon, prostate, ovary, uterus and endometrial malignant tissue as well as in endemetrial metastases. See, Tables 3 and 9 below. This is similar to other examples of specific gene expression in tumors, such as in the case of the PSA gene which is expressed as a reliable biomarker for prostate cancer, but is also expressed in breast cancer. See, Diamandis EP & Yu H., Urol. Clin. North Amer. 24:275-282 (1997). Moreover, the HER-2/new gene, a biomarker for breast cancer, was found to be amplified in non-diploid prostate cancers, when compared with diploid prostate cancers. The present work primarily concentrated on liver diseases, such as cirrhosis and HCC. An analysis of 30 liver disease cases for MAG expression indicated its importance in liver neoplasias. The absence of expression of MAG gene in normal tissues and its presence in various malignancies further supports a role of the MAG gene in malignant transformation.

The terms "nucleic acid" and "polynucleic acid" refer herein to deoxyribonucleic acid and ribonucleic acid in all their forms, i.e. single and double-stranded DNA, cDNA, mRNA, and the like. As used herein, the term "encode" in its various grammatical forms includes nucleotide and/or amino acids which correspond to other nucleotide or amino acids in the transcriptional and/or translational sense. The phrase "liver neoplastic disease" refers herein to diseases which are characterized by the development of abnormal tissue growth in the liver. Liver neoplastic diseases include, for example, hepatocellular carcinoma, adenomatous hyperplasia, adenoma of the liver, and the like. The cirrhotic liver (cirrhosis caused by or associated with alcohol, hepatitis B and C viruses) is a substrate for the development of HCC (about 80-90% of HCC develops in cirrhotic patients).

The polynucleotide of the invention comprises an oligonucleotide which encodes an oligopeptide of SEQ. ID NO: 2 shown in Table 1 below, SEQ. ID NOS: 8 and 9 shown in Table 7 below, SEQ. ID NO: 23 shown in Table 12 and/or antibody binding fragments thereof about 7 to 80 amino acids long.

Table 1: Liver Neoplastic Disease Polynucleotide & polypeptide Sequence Fragments TGGTCCTTTG GCGTCGTCCT CAA GTT ATA TTA GAA TCG TGT CCT CCC AGC 50

Val lie Leu Glu Ser Cys Pro Pro Ser 1 5

TTT GGC CAG CTT ACT ATT CTA GGA CTT GAT TCC TTC ATT CAG TCA CAA 98 Phe Gly Gin Leu Thr He Leu Gly Leu Asp Ser Phe He Gin Ser Gin 10 15 20 25

TTT ATT GAG CAC CGA CTT TGC ATC AAG CTC TTG CTG AAG ATA ACG CTG 146 Phe He Glu His Arg Leu Cys He Lys Leu Leu Leu Lys He Thr Leu

30 35 40

ATG ATG AG (SEQ. ID NO:l) 154 Met Met (SEQ. ID NO: 2) 43

The polynucleotide of this invention may consist of about 21, 36, 50, 75 to about 154, 240, 360, 569, 1500 nucleotides long. In another embodiment, the polynucleotide of this invention may also comprise oligonucleotides complementary to these sequences and their fragments which hybridize to the gene sequences, preferably under stringent conditions as is known in the art and described by Sambrook et al

(1989) in the Manual of Laboratory procedures referenced below. These polynucleotides, thus, may be applied to the assessment of the presence of the gene in biological samples by hybridization under moderate or stringent conditions, as is .known in the art. As used herein, when the phrase "substantially the same" is used in conjunction with nucleic acid sequences, it refers to nucleic acid sequences having conservative substitutions (or non-consequential substitutions) as compared to the reference sequence. For example, substitutions in nucleotide sequences that do not substantially alter the function of the protein it encodes, or the tertiary structure of that protein, would be considered to produce a nucleic acid sequence that is substantially the same as the reference sequence. The present invention encompasses all degenerate nucleotide sequences which encode the polypeptide of the invention due to the redundancy of the DNA code, as well. When the phrase "substantially the same" is used in conjunction with amino acid sequences, it refers to amino acid sequences that result from substitutions that do not substantially alter the function of the protein or its tertiary structure. For example, substitution of a charged amino acid residue for a similarly charged amino acid residue or substitution of a non-polar amino acid residue for another non-polar amino acid residue would typically be considered to produce an amino acid sequence that is substantially the same as the reference sequence.

An example of the polynucleotide of the invention is provided as SEQ. ID NO: 1 shown in Table 1 above. This oligonucleotide encodes a protein associated with ciirhosis and neoplastic liver diseases, such as hepatocellular carcinoma, but not normal liver. The SEQ. ID NOJ is 154 base pairs ("bp") long and contains an open reading frame that extends from nucleotide 24 to 132 of SEQ ID NO: 1. Another example is the polynucleotide of SEQ. ID NO: 7 shown in Table 6 below, and the encoding region extends from nucleotide 24 to 134 of SEQ. ID NO: 7. Still another example is the polynucleotide of SEQ. ID No:22 shown in Table 11 below. Sequence searches conducted of the GenBank data base indicated that the polynucleic acid sequences set forth in SEQ ID NOJ, SEQ. ID NO: 7 and SEQ. ID NO:22 are novel sequences, and that they correspond to a novel gene. Set forth as SEQ ID NO:2, SEQ. ID NOS: 8 and 9 and SEQ. ID NO:23 are deduced amino acid sequences of fragments encoded by SEQ. ID NO: 1 and SEQ. ID NO: 7 fragments. A detailed description of the experimental methods used to demonstrate the association between the expression of the polynucleic acid sequences set forth in SEQ. ID NOJ , SEQ. ID NO: 7 and SEQ ID NO:22, and neoplastic disease is provided in the exemplary section set forth below. Fragments to about 75, 100, 150, 200 are part of a preferred embodiment of the nucleic acid described in this patent.

The present invention further relates to nucleotide probes and primers that are sufficiently complementary to the above-described sequences to hybridize thereto under moderately stringent conditions, and more preferably under high stringency conditions, as well as to permit the amplification of the polynucleotide by, for instance, polymerase chain reaction (PCR). Exemplary probes include oligomers that are at least about 15 consecutive nucleotide long, preferably at least about 40 nucleic acid residues long and that are selected from any contiguous fragments of the polynucleotides of the present invention. Preferred oligomeric probes used in the practice of the present invention may be at least about 60 nucleotide long. The present invention also contemplates oligomeric probes that are 150 nucleic acid residues long or longer. However, any length oligonucleotides which are effective in hybridizing to the gene and mRNA sequences associated with neoplastic liver ailments are within the four corners of this patent. Those of ordinary skill in the art realize that nucleic acid probe technology is well known and that suitable hybridization conditions for achieving the hybridization of a probe of a particular length to polynucleotides of the present invention may be readily determined. Such manipulations to achieve optimal hybridization conditions for probes of varying lengths are well known in the art. See, e.g. Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor (1989), the relevant portions of which are incorporated herein by reference. The oligomeric probes\primers of the present invention are preferably labeled to render them readily detectable. Detectable labels may be any species or moiety which may be detected either visually or with the aid of an instniment. Commonly used detectable labels are radioactive labels such as, for example, ³²P, ^l C, ¹²⁵1, ³H, ^MS, and the like. Biotin labeled nucleotide can be incorporated into DNA or RNA by such techniques as nick translation, chemical and enzymatic means, and the like. The biotinylated probes are detected after hybridization using indicating means such as avidin/streptavidin, fluorescent labeling agents, enzymes, colloidal gold conjugates, and the like. The nucleic acids of the invention also may be labeled with other fluorescent compounds, with immunodetectable fluorescent derivatives, with biotin analogues, and the like. Nucleic acids may also be labeled by means of attachment to a protein. Nucleic acids cross-linked to radioactive or fluorescent single-stranded histone binding protein may also be used. Those of ordinary skill in the art will recognize that there are other suitable methods for detecting oligomeric probes and other suitable detectable labels that are available for use in the practice of the present invention.

In another embodiment, the present invention relates to constructs that include the polynucleotide, probe and/or primer described above, an origin of replication, and a promoter. The constructs of the invention are useful to introduce polynucleic acid sequences into host cells for either expression (protein production) or replication (amplification of nucleic acids). The methods for selection and use of such constructs are well known to those of ordinary skill in the art and will vary in accordance with the cell targeted to receive the polynucleic acid. See, e.g. Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor (1989). The present nucleic acids may also be cloned into a vector, either eukaryotic or prokaryotic, for amplification and/or expression purposes. The techniques for these procedures are known in the art.

The introduction of the above-described constructs and vectors into appropriate host cells enables the amplification and expression of the cloned polynucleic acid sequence. Appropriate expression vehicles are well known to those of ordinary skill in the art and include those that are replicable in eukaryotic cells and/or prokaryotic cells and those that remain episomal or those which integrate into the host cell genome. See, e.g., Sambrook et al., above. Presentiy preferred vehicles for expression of the invention gene sequences in eukaryotic host cells, particularly mammalian cells, include Rexp with, for instance, an RSV LTR, Moloney murine leukemia virus LTR driven expression vector, and the like. As used herein, a "promoter region" refers to a segment of polynucleic acid that controls transcription of DNA to which it is operatively linked. The promoter region includes specific sequences that are sufficient for RNA polymerase recognition, as well as binding and transcription initiation. This portion of the promoter region is referred to as the promoter. In addition, the promoter region includes sequences that modulate the recognition, binding and transcription initiation activity of RNA polymerase. Depending upon the nature of the desired type of regulation, the promoters may be constitutive or regulated. Promoters contemplated for use in the practice of the present invention include the SV40 early promoter, the cytomegalovirus (CMV) promoter, Moloney murine leukemia virus (MMLV) promoter, thymidine kinase promoter, albumin promoter, Rous Sarcoma virus promoter (RSV), and the like. As used herein, the term "operatively linked" refers to the functional relationship of polynucleic acid sequences with regulatory and effector sequences of nucleotide, such as promoters, enhancers, transcriptional and translational stop sites, and other signal sequences. For example, operative linkage of DNA to a promoter refers to the physical and functional relationship between the DNA and the promoter such that the transcription of such DNA is initiated from the promoter by an RNA polymerase that specifically recognizes, binds to and transcribes the DNA.

The vectors and constructs are also provided as host cells containing them. Host cells contemplated for the practice of the invention are, for example, bacterial, yeast and mammalian cells which may be used for replicating polynucleic acids of the present invention and producing the same, or substantially the same polypeptide as set forth in SEQ. ID NO: 2, SEQ. ID NO: 8, SEQ. ID NO: 9 and SEQ ID NO:23 under effective expression conditions. Methods and conditions suitable to promote expression are well .known in the art. See, e.g. Sambrook et al., (1989) above. The heterologous polynucleotide of the inventions may be introduced into host cells by any method .known to those of skill in the art, such as for example, transfection with a vector encoding the heterologous DNA by CaP0₄ precipitation. See, e.g., Kashanchi, F., et al., Nucleic Acids Research, 20:4673-4674 (1992).

The polypeptide of the invention comprises an oligopeptide that is encoded by the polynucleotide of the invention and fragments thereof about 7 to 80 , preferably about 10 to 57, more preferably about 15 to 57, and still more preferably 20 to 36 amino acids long. Some of the more preferred fragments are those about 36 and 57 amino acids long, which are representative of the peptides characteristically expressed in individuals afflicted with cirrhosis and neoplastic liver diseases, such as HCC, and by fetal tissues, but not in individuals with normal, non-neoplastic liver function. Suitable oligopeptides include those having the same, or substantially the same sequence as that set forth in SEQ ID NO 2, SEQ. ID NOS: 8 and 9, and SEQ. ID NO: 23, or antibody binding fragments thereof about 7 to 80 amino acids long. As used herein, the terms "protein", "peptide" and "polypeptide" are considered to be equivalent terms and are used interchangeably. The polypeptide is are also provided in their salt form, preferably as a biologically acceptable salt, and more preferably as a pharmaceutically acceptable salt, and as mixtures thereof as well as with the proteins themselves.

The invention further provides antibodies that bind to the polypeptide of this invention, or substantially the same polypeptide set forth in SEQ. ID NO:2, SEQ. ID NO: 8, SEQ. ID NO:9 and/or SEQ. ID NO:23. Such antibodies are suitable for use in the diagnosis, prevention and treatment of liver neoplastic diseases. In this context, the term "antibody" encompasses monoclonal antibodies and polyclonal antibodies, and among the monoclonal antibodies more preferred are humanized antibodies. For example, preferably for therapeutic applications, the antibodies employed are preferably humanized antibodies to minimize the human antibody reaction to antibodies from other species. The above-described antibodies may be prepared employing standard techniques that are well known to those of sltill in the art, using the same, or substantially the same protein as set forth in SEQ. ID NO:2, SEQ. ID NO: 8, SEQ. ID NO:9, SEQ. ID NO:23, or fragments thereof, as antigens for antibody production. Polyclonal antibodies of the present invention are typically produced by immunizing a mammal with an inoculum containing the same, or substantially the same proteins as set forth in SEQ ID NO 2, SEQ. ID NO: 8, SEQ. ID NO:9 and/or SEQ. ID NO:23 or fragments thereof, thereby inducing in the mammal, antibody molecules having immunospecificity for the protein set forth in SEQ. ID NO:2, SEQ. ID NO: 8, SEQ. ID NO:9 and/or SEQ. ID NO:23 or fragments thereof. To enhance their specificity, the antibodies may be purified, for example, by immunoaffinity chromatography using solid phase-affixed immunizing polypeptide. Their purification is, thus, achieved by contacting antibody with the solid phase-affixed immunizing polypeptide for a time sufficient for the polypeptide to immunoreact with antibody to foim a solid phase-affixed immunocomplex. The bound antibodies are then separated from the complex by standard techniques. Monoclonal antibody production typically proceeds by isolating lymphocytes and fusing them with myeloma cells, thus producing hybridomas. The cloned hybridomas are then screened for production of antibodies specific for the same, or substantially the same protein as set forth in SEQ ID NO 2, SEQ. ID NO: 8, SEQ. ID NO:9 and/or SEQ. ID NO:23 or fragments thereof described above. The thus produced antibody may be provided in the foπn of a composition and a ltit, with instnictions for its use in the detection of the protein as well as applied in diagnostic and assay methods to detect the presence or absence of protein associated with liver neoplastic disease by detecting the presence of the polypeptide and/or the antibody and for screening populations to determine the subjects' susceptibility to neoplastic liver disease. Such methods may comprise contacting a biological sample with the antibody (or protein) of the invention under conditions effective to form complexes of the antibody and the protein associated with liver neoplastic disease is formed; and then detecting the presence of the resulting complex. The presence of a complex is indicative of susceptibility to neoplastic liver disease. Suitable "biological samples" include tissues, such as any liver tissue, or cells, such as a hepatocytes, and the like. Preferred antibodies of the present invention are detectably labeled to facilitate the identification of the presence of antibody-protein complex. Antibodies may be labeled with a variety of detectable compounds. For example, the detectable label may be a fluorescent labeling agent that chemically binds to antibodies without denaturing them to form a fluorochrome (dye) that is a useful immunofluorescent tracer. Suitable fluorescent labeling agents are fluorochromes such as fluorescein isocyanate (FIC), fluorescein isothiocyanate (FITC), 5- dimethylamino-1-naphthalenesulfonyl chloride (DANSC), tetramethylrhodamine isothiocyanate (TRITC), lissamine, rhodamine 8200 sulphonyl chloride, and the like. A description of immunofluorescence analysis techniques is found in DeLuca, "Immunofluorescence Analysis", in Antibody as a Tool, Marchalonis et al., eds., John Wiley & Sons, Ltd., pp. 189-231 (1982), the relevant portion of which is incorporated herein by reference. Radioactive elements are also useful detectable labels. An exemplary radiolabeling agent is a radioactive element that produces gamma ray emissions. Elements which themselves emit gamma rays, such as ¹²⁵I and ¹³¹I, represent one suitable class of gamma ray emission-producing radioactive element indicating groups. In one embodiment, the detectable label is an enzyme, such as horseradish peroxidase (HRP), glucose oxidase, and the like. In such cases where the detectable marker is an enzyme (such as HRP or glucose oxidase), additional reagents are typically required to indicate that the antibody-protein complex has formed. Such additional reagents for HRP include hydrogen peroxide and an oxidation dye precursor such as diaminobenzidine, o-phenylenediamine dihydrochloride and the like. An additional reagent useful with glucose oxidase is 2,2'-azino-di-(3-ethyl-benzthiazoline-G-sulfonic acid). Depending on the nature of the label or catalytic signal producing system used, a signal may be detected by irradiating the complexed test sample with light and observing the level of fluorescence; by contacting the complexed sample with a substrate which can be catalytically converted by the label to produced a dye, fluorescence or chemiluminescence, in which the formation of dye can be observed visually or in a spectrophotometer; or, in the case of chemiluminescence or a radioactive label, by employing a radiation counter such as a gamma counter or gamma emitting labels such as ¹²⁵I. For detection of enzyme-catalyzed labels when the presently preferred combination of HRP is used as the enzyme and o-phenylenediamine dihydrochloride as the substrate, a quantitative analysis of complex can be made using a spectrophotometer (for example a EMAX Microplate Reader; available from Molecular Devices, Menlo Park, CA) at 405 nm in accordance with the manufacturer's instructions. One method for detecting the presence of antibody-bound complex employs an "ELISA" format that provides for the detection and quantification of either antibody or antigen (depending on the ELISA format type) present in a sample. ELISA format is a well-known technique that can be readily carried out by those of ordinary skill in the art. A description of the ELISA technique is found in Chapter 22 of the 4th Edition of Basic and Clinical Immunology, by D.P. Sites et al., published by Lange Medical Publications of Los Altos, CA in 1982, incorporated herein by reference. Useful solid matrices are also well known in the art. Such materials are water insoluble and include cross-linked dextran (available from Pharmacia Fine Chemicals; Piscataway, NJ); agarose; polystyrene beads (typically about 1 micron to about 5 millimeters in diameter; available from Abbott Laboratories; North Chicago, IL); polyvinyl chloride; polystyrene; cross-linked polyacrylamide; nitrocellulose- or nylon-based webs such as sheets, strips or paddles; or tubes, plates or the wells of a microtiter plate, such as those made from polystyrene or polyvinylchloride; and the like.

The polynucleotides of the invention also encompass anti-sense oligonucleotides and polynucleotides comprising the anti-sense oligonucleotides. As contemplated in the practice of the present invention, anti-sense oligonucleotides, and polynucleotides comprising the anti-sense oligonucleotides, may be readily prepared as is .known in the art. These anti-sense molecules bind to and, therefore, block the synthesis of the RNA encoding the protein of the present invention. Thus, the anti-sense polynucleotides and oligonucleotides may be administered to a subject to inhibit the development of a variety of malignant tissues such as tumorcidal agents for cirrhosis and other liver neoplastic diseases, such as HCC, breast cander, lung cancer, etc. See, Table 9 below. One of ordinary sltill in the art will appreciate that when compositions, e.g., antibodies, antisense oligonucleotides, or DNA sequences encoding anti-sense oligonucleotides, of the present invention are administered as therapeutic agents, it may be necessary to combine these compositions with other suitable components to form a suitable pharmaceutical composition. The particular composition will depend on the intended use and mode of administration.

The present invention provides pharmaceutical compositions useful for practicing the therapeutic methods described herein. These pharmaceutical compositions of the present invention may contain a physiologically or pharmaceutically acceptable carrier together with anti-sense oligonucleotides, polynucleotides comprising anti-sense oligonucleotides, proteins or antibodies, as described herein, dissolved or dispersed therein as an active ingredient. In a preferred embodiment, the pharmaceutical composition is not immunogenic when administered to a subject such as a mammal or a human subject, for therapeutic purposes. This may be accomplished, for example, by commonly known techniques of "humanizing" antibodies wherein the constant regions of an antibody derived from a non-human animal is replaced with constant regions from a human. As used herein, the term "pharmaceutically acceptable" and grammatical variations thereof, as they refer to compositions, carriers, diluents and reagents, are used to represent that the materials are capable of administration to a mammal without the production of undesirable physiological effects such as nausea, dizziness, gastric upset, and the like. The preparation of a pharmaceutical composition that contains active ingredients dissolved or dispersed therein is well known in the art. Typically, such compositions are prepared as injectables either as liquid solutions or suspensions; however, solid forms suitable for solution, or suspension in liquid prior to use can also be prepared. The preparation can also be emulsified. The active ingredient may be mixed with excipients which are pharmaceutically acceptable and compatible with the active ingredient and in amounts suitable for use in the therapeutic methods described herein. Suitable excipients are, for example, water, saline, dextrose, glycerol, ethanol, and the like, as well as combinations of any two or more thereof. The therapeutic composition of the present invention may include pharmaceutically acceptable salts of the components therein. Pharmaceutically acceptable nontoxic salts include the acid addition salts (formed with the free amino groups of the polypeptide) that are formed with inorganic and organic acids such as, for example, hydrochloric acid, hydrobromic acid, nitric acid, sulfuric acid, phosphoric acid, acetic acid, propionic acid, glycolic acid, lactic acid, pyruvic acid, oxalic acid, malonic acid, succinic acid, maleic acid, fumaric acid, anthranilic acid, cinnamic acid, naphthalene sulfonic acid, sulfanilic acid, and the like, as well as combinations of any two or more thereof. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium hydroxide, ammonium hydroxide, potassium hydroxide, and the like; organic bases such as mono-, di-, and tri-alkyl and -aryl amines (e.g., triethylamine, diisopropyl amine, methyl amine, dimethyl amine, and the like); ethanolamines (e.g., ethanolamine, diethanolamine, and the like); and the like, as well as combinations of any two or more thereof. Physiologically acceptable carriers are well .known in the art. Exemplary of liquid carriers are sterile aqueous solutions that contain no materials in addition to the active ingredients and water, or contain a buffer such as sodium phosphate at physiological pH value, physiological saline or both, such as phosphate-buffered saline. Still further, aqueous carriers can contain more than one buffer salt, as well as salts such as sodium and potassium chlorides, dextrose, polyethylene glycol and other solutes. Liquid compositions can also contain liquid phases in addition to (or to the exclusion of) water. Exemplary of such additional liquid phases are glycerin, vegetable oils such as cottonseed oil, water-oil emulsions, and the like. A "therapeutically effective" amount is a predetermined amount intended to achieve the desired effect, such as the inhibition of the development of neoplastic liver disease. The required dosage for inhibiting neoplastic disease will depend on a variety of factors, including age, weight, sex and medical condition of the patient, as well as the severity of the pathology, the route of administration, and the type of therapeutic agent used. A sltilled physician or veterinarian can readily determine and prescribe the effective amount of the pharmaceutical composition required to treat the patient. Conventionally, one of ordinary skill in the art would employ relatively low doses initially and subsequently increase the dose until a maximum response is obtained. Kits for use in screening for susceptibility for liver neoplastic disease are also provided by the present invention. Such kits may include all or some of the reagent primers, probes, antibodies, proteins and/or anti-sense oligonucleotides described herein for determining the presence or absence of the polynucleotides, antibodies and/or proteins associated with liver neoplastic disease, and instructions for their use for the intended purpose. The .kits of the present invention may further contain, for example, restriction endonuclease, one or more labeled cDNA probes, lyophilized antibody that is capable of binding to proteins of the present invention, lyophilized secondary antibodies that are conjugated to a fluorochrome or peroxidase (in combination with an appropriate amount of hydrogen peroxide substrate) and that are capable of binding antibodies that are reactive to proteins of the present invention, blocking solutions (e.g., normal goat or rabbit serum, 3% bovine serum albumin solution in physiological saline, and the like), or buffers (e.g., Tris-HCl, phosphate, EDTA, and the like).

The invention will now be described in greater detail by reference to the following non- limiting examples.

EXAMPLES Example 1: Characterization and Preparation of Liver Tissue Samples Human liver tissue samples were obtained from the Department of Pathology at Cedars-Sinai

Medical Center in Los Angeles, CA. The study group included 28 men and 8 women, ranging in age from 4 years to 76 years of age (mean age 47.6 years). None of these individuals had distant metastasis or had been previously treated for HCC. All of the individuals had undergone liver biopsy and/or surgery within two years prior to the study. The tissue specimens were taken from the liver biopsy samples. All specimens were fixed in neutral buffered formalin and embedded in paraffin blocks, according to the method described by Greet, C.E., et al., "PCR Amplification from Paraffin-Embedded Tissues," Anatomic Pathology, 95: 117- 124 (1991).

Histological diagnosis of the tumors was verified by an experienced pathologist. The pathology results for this study group indicated the following: 1) 4 normal liver samples; 2) 9 samples positive for chronic liver disease caused by hepatitis C virus (HCV) (6 of these were also positive for liver cirrhosis and 3 were also positive for chronic active hepatitis (CAH)); and 3) 12 samples positive for alcoholic liver disease (ALD) (4 of these were also positive for HCV, 2 were also positive for liver adenoma, and 9 were also positive for HCC).

Example 2: Extraction of mRNA from Liver Tissue

Messenger RNA was extracted from the liver biopsy samples of Example 1 using a modification of the acid guanidinium thiocyanate/phenol/chloroform method described by Chomczynski and Sacchi, .Anal. Biochem., 162: 156-157 (1987). Specifically, crashed, frozen liver tissue biopsy samples from Example 1 were placed into test tubes. A 0.5 ml aliquot of a solution of 4 M guanidine thiocyanate, 25 mM sodium citrate (pH 7.0), 0.5 % N-lauroylsarcosine, and OJ M 2-mercaptoethanol was added to the tissue sample in each test tube. The test tubes were agitated for up to 24 hours at room temperature. The following aliquots were added to each tube: 1) OJ ml of a chloroform/isoamyl alcohol 24: 1 v/v solution; 2) 0.5 ml of acid phenol; and 3) 50 μ\ of sodium acetate. The tubes were then centrifuged at a centrifugation rate of 12,000 x G for 20 minutes to pellet the tissue. The aqueous phase from each tube was transferred by pipet into a clean tube. An aliquot of 1.5 ml of ethanol was added to the aqueous phase in each tube to precipitate the RNA. The tubes were allowed to stand on a test tube rack at -80°C for 2 hours, then centrifuged again at a centrifugation rate of 12,000 x G for 20 minutes to generate an RNA pellet.

The pellets were each washed with a 1 ml aliquot of 75% ethanol. After washing, the pellets were air-dried at room temperature for 5 minutes. The pellets were then resuspended in digestion buffer (10 mM Tris-HCl and 2 mM ethylenediamine tetraacetic acid (EDTA)), then treated with 20 units (U) of DNase- free RNase (Sigma Chemical Co., St. Louis, MO) for 30 minutes at 37°C. To remove the DNase-free RNase, the phenol/chloroform extraction procedure was repeated a second time on the pellet, immediately followed by ethanol precipitation, as described above. After the precipitation step, the pellets were washed in distilled water.

The optical density of RNA in distilled water was measured at wavelengths of 260 nm and 280 nm using a Beckman, DU 640 Spectrophotometer (U.S.A.). The OD₂₆₀/OD₂₈₀ ratio was used to quantitate the amount of RNA extracted and to determine the purity of each preparation. Example 3: Amplification of cDNA

Reverse transcription of 1 μg of each mRNA sample from Example 2 and amplification of the resulting cDNA by polymerase chain reaction (PCR) was carried out using the GeneAmp^® RNA PCR Kit (Perkin-Elmer-Cetus, Norwalk, CT) according to the manufacturer's directions. For reverse transcription, oligo d(T)_l6 (Perltin-Elmer-Cetus, Norwalk CT) was used to prime the synthesis of cDNA. For PCR amplification of the reverse transcribed cDNA, the primers shown in Table 2 below, identified as SEQ ID NO 3 ("upstream primer") and SEQ ID NO 4 ("downstream primer") were used. Table 2: Amplification Primers

SEQ. ID NO: 3 TGGTCCTTTG GCGTCGTCCT C SEQ. ID NO: 4 CTCATCATCA GCGTTATCTT C

Two negative controls were used: 1) a sample containing water only; and 2) a sample devoid of RNA template, but otherwise containing all of the reverse transcription and PCR reagents. In addition, an RT-PCR positive control of RNA from pAW109, in 1 mM EDTA, 10 mM NaCl, 30 μg/ml E. Coli rRNA, and 10 mM Tris-HCL (pH 8) (all of which were provided in the GeneAmp^® RNA PCR kit) was used. The GeneAmp^® PCR System 9600 (Perkin-Elmer-Cetus, Norwalk, CT) thermal cycler was used to control the PCR reactions. Programmable temperature cycling was performed with the following cycle profile: 94°C for 1 minute, then 35 cycles of each of the following: 1) denaturation for 30 seconds at 94°C; 2) annealing for 45 seconds at 55°C; and 3) extension for 45 seconds at 72°C. After 35 cycles, the reaction tubes were incubated at 72° for 5 minutes, then cooled to 4°C. The amplified cDNA samples were characterized by electrophoresis on gels containing 3%: 1 % NuSieve:Seakemagarose (FMC, Rockland, ME) at room temperature for 2 hours.

A search in the Genbank and EMBL nucleic acid sequence libraries using the Intelligenetics Suite (Intelligenetics, Inc., Mountain View, CA) program indicated that these primers would not hybridize to any other known nucleic acid sequences under the conditions used. Example 4: Sequencing of Marker Gene

Sequencing of the marker gene was conducted according to the Sanger method of sequencing. Bands were cut from the gel used in Example 3 and sequenced using a Sequenase kit (United States Biochemical, Cleveland, OH) containing DNA polymerase (United States Biochemical, Cleveland, OH) and (³⁵S)dATP (Amersham, Arlington Heights, IL) according to the manufacturer's directions. Plasmid template CDNA was prepared for sequencing according to a commercial protocol provided by Promega Biotec (Madison, WI). The gels were photographed onto Kodak Diagnostic Film SB 100 (Rochester, NY). An IBI Standard Sequencer, Model STS 45 (New Haven, CT) was used to sequence the gels.

A 154 base pair polynucleic acid was isolated and compared with known sequences in Genbank. No known gene matched this sequence. The sequence of this novel polynucleic acid is set forth as SEQ ID NO 1. The amino acid sequence predicted by this nucleic acid sequence is set forth in SEQ ID NO 2. Analysis of the predicted protein showed an open reading frame extending from bp 24 to bp 132 of the nucleic acid sequence set forth in SEQ ID NO 1. Example 5: Preparation of cDNA Probe for Detecting Gene Product

Primers were selected to isolate and amplify a cDNA probe complementary to cellular mRNA associated with the polynucleotide sequence set forth in SEQ ID NO 1. The primers identified in Table 3 below as SEQ. ID NO: 5 ("upstream primer") and SEQ. ID NO: 6 ("downstream primer") were used in the polymerase chain reaction method described in Example 3 above. Table 3: cDNA Probe Primers

SEQ. ID NO: 5 AAGTTATATT AGAATCGTGT C SEQ. ID NO: 6 CAAGAGCTTG ATGCAAAGTC G

The isolated cDNA probe was characterized by electrophoresis on a 3 %: 1 % NuSieve:Seakemagarose gel as described in Example 3 above, then sequenced according to the method described in Example 4. The amplified cDNA probe was 101 base pairs long and the sequence corresponded to a portion of the 154 base pair cDNA that was isolated in Example 3.

Example 6: Screening of Normal and Diseased Liver Tissue by RT-PCR

Expression of the polynucleotide sequence identified in Example 4 was studied in 18 fresh- frozen liver biopsy samples by RT-PCR. Liver biopsy samples with the following pathologies were screened: 4 normal liver samples; 1 fulminant liver samples; 7 cirrhotic liver samples (2 with small HCC nodules), and 6 HCC liver samples. Messenger RNA was extracted from these samples as described in Example 2. RT- PCR was conducted to obtain amplified cDNA product using the methods described in Example 3 above. As in Example 5 above, primers used for PCR amplification are set forth in SEQ ID NO 5 ("upstream primer") and SEQ ID NO 6 ("downstream primer"). The cDNA obtained from each liver biopsy sample was characterized by electrophoresis on gels containing 3%: 1 % NuSieve:Seakemagarose (FMC, Rockland, ME) at room temperature for 2 hours.

The results indicated that the normal and fulminant liver samples did not contain any cDNA associated with expression of the novel gene sequence set forth as SEQ ID NO 1. In contrast, cDNA associated with this novel gene sequence was detected in all of the cirrhotic liver samples, and 5 of the 6 HCC liver samples. These results confirmed that the novel gene is expressed in cirrhotic and HCC liver tissue, but not in normal liver tissue. Thus, this novel gene is a useful marker for screening for liver diseases such as cirrhosis and HCC. Example 7: Screening of Various Types of Tissue Samples for Gene Expression

Using the method described in Example 1 , mRNA was extracted from tissue samples from the following human tissues: 2 placentas, 1 normal kidney, 2 normal livers, 1 breast carcinoma, 1 spleen from a patient with lymphocytic leukemia and 2 livers with HCC. Complementary DNA was obtained from the mRNA by RT-PCR, as described in Example 3. The cDNA obtained from each tissue sample was characterized by electrophoresis on an agarose gel as described in Example 3.

Complementary DNA associated with the expression of the novel gene described in Example 4 was detected in tissue samples obtained from breast carcinoma, a spleen from a patient with lymphocytic leukemia, and the 2 liver tissue samples afflicted with HCC. In contrast, the cDNA associated with the novel gene was not detected in any of the tissue samples from normal, non-cancerous placenta, kidney and liver tissue. The absence of expression of the novel gene in noπnal tissue tested suggests that this gene may play an important role in the process of malignancy. Example 8: Tissue Expression of Marker Gene

Messenger RNA is extracted from tissue samples as described in Example 2. The extracted mRNA is resolved on a 1.5% agarose-formaldehyde gel by applying 18 mAmps for 16 hours. The extracted mRNA is then transferred to a nylon membrane (Schleicher & Schull, Keene, NH) by capillary action. The transferred mRNA is fixed onto the membrane by exposing the mRNA and nylon membrane to short-wave ultraviolet radiation in a Stratalinker (Stratagene, La Jolla, CA) for 40 seconds according to the manufacturer's directions. The membranes are pre-hybridized for 1 hour at 42 °C with a solution of 50% deionized formamide, 7% sodium dodecyl sulfate (SDS), 10% bovine serum albumin (Sigma, St. Louis, MO), 1 mM EDTA and 0.2 M sodium phosphate (pH 7.2). The 101 bp cDNA probe for the novel gene, described in Example 5, is radiolabeled with ³²P by random primer oligolabeling in the presence of dCT(α³²P). The nylon membranes are hybridized in the presence of the ³²P-cDNA probes by adding the probes to the pre- hybridization solution for a hybridization period of 16 hours at 42°C. After hybridization, the membranes are briefly washed three times in a solution of 40 mM sodium phosphate, 1 mM EDTA, and 1 % SDS at 64 °C for three short washes, followed by a final 1 hour wash. The membranes are exposed to pre-flashed Kodak XAR-5 film (Rochester, NY) at -70°C for 2 to 14 days.

A positive signal indicates the presence of marker gene-specific mRNA expressed in the respective tissue.

Example 9: Polyclonal Antibodies against Marker Gene Product

Peptides synthesized according to the sequence set forth in SEQ ID NO 2 are conjugated to keyhole limpet hemocyanin (KLH) and bovine serum albumin (BSA) according to the manufacturer's instructions (Imgect, Immunogen Conjugation Kit from Pierce Chemical Co., Rockford, IL). Immunogen is prepared by mixing KLH-conjugated peptides thoroughly with Freund's complete adjuvant (Pierce Chemical Co., Rockford, IL) in a 1: 1 v/v ratio. A dose of 100-200 μg of the immunogen is then injected subcutaneously in 10 sites in 3 young New Zealand White rabbits per peptide. Just prior to immunization, 5-10 ml of preimmune blood is collected through the ear vein. On days 14 and 28, the rabbits are boosted by the same injection route using immunogen in incomplete Freund's adjuvant. Starting from day 28, blood is collected twice a week (up to 30 ml each time) for up to 3 months and assayed by standard peroxidase/DAB-based ELISA (kit from Pierce) against BSA-conjugated peptide, with preimmune serum as a negative control. Sera from positive bleeds are pooled and IgG is isolated by protein A-agarose (Sigma, St. Louis, MO) affinity chromatography. Immune IgG is further purified by affinity chromatography on columns with peptide immobilized on agarose beads. Purified IgG is tested for reaction by immunoprecipitation, Western blotting and immunohistochemistry. Example 10: Monoclonal Antibody against Marker Gene Product

Peptides synthesized according to the sequence set forth in SEQ ID NO 2 are conjugated to keyhole limpet hemocyanin (KLH) and bovine serum albumin (BSA) according to the manufacturer's instructions (Imgect, Immunogen Conjugation Kit from Pierce Chemical Co., Rockford, IL). One month old Balb/c mice (10 mice per peptide) are bled through the tail vein on day one and immunized intraperitoneally using 20-100 μg KLH-peptide complex (day one, in complete Freund's adjuvant (Pierce Chemical Co., Rockford, IL); day 14, in incomplete Freund's adjuvant (Pierce Chemical Co. Rockford, IL); day 28, in incomplete Freund's adjuvant). On day 35, the injection is given intravenously without adjuvant. If only BSA-peptide complex is soluble, it is injected instead of the KLH-peptide complex. On day 38, the mice are sacrificed by cervical dislocation, the splenocytes removed, washed in cold Dulbecco' s MEM (DMEM) without serum and fused with mouse myeloma X-63 Ag 8.563 at 37°C for 1.5 minutes using polyethylene glycol (PEG), molecular weight 1,500 (Merck, NJ.).

After washing out the PEG three times in DMEM with 10% bovine serum, cells are seeded in DMEM with 20% fetal bovine serum and HAT supplement on 96 well plates with preseeded feeder splenocytes from normal mice (one normal feeder spleen for 4 plates, and one immune spleen for 6 plates).

The cultures are left for 7-10 days. Culture medium is changed once a week until clonal growth is observed.

Positive hybridoma clones are assayed by indirect immunofluorescence on HCC tissue sections and/or ELISA and propagated until enough antibody is collected. Positive hybridomas are frozen during subculture on a weekly basis. Example 11: Expression of Human Malignancy Associated Gene (MAG) is Expressed in Liver Cirrhosis and Various Tumors

Human tissues were obtained from the Department of Pathology of Cedars-Sinai Medical

Center, and tumor hepatocyte cell cultures HepG2 and Hep3B were purchased from American Type Culture

Collection (Rockville Pike, MD). Gene sequencing was conducted with a Sequenase kit, based on the method of Sanger et al. , including

Sequenase DNA polymerase from United States Biochemical (Cleveland, OH). See, Sanger et al., PNAS (USA) 7 (4): 5463 (1977). ³⁵S-dATP was obtained from Amersham (Arlington Heights, IL). Our sequencing gels were run on an IBI Standard Sequencer STS 45 (New Haven, CT).

Plasmid template 154 bp cDNA was prepared for sequencing according to the Promega Biotech (Madison, WI) commercial protocol.

The preparation of tissue mRNA was conducted as follows. Total RNA (50-100 (g) was isolated using TRIzol reagent (Life Technologies, Gaithersburg, MD). The tissue was homogenized in TRIzol solution at 4° C (1 ml TRIzol for 100 mg of tissue). After 5 min. incubation at room temperature, 0.2 ml of chloroform was added per 1 ml of TRIzol. The RNA pellets were washed with 75% ethanol, air dried and treated with 20 U of DNase RNase-free (Sigma Chemical Co., St. Louis, MO). The OD₂₆₀/OD₂₈₀ ratio was determined spectrophotometrically for RNA quantitation. Poly(A)-containing RNA was prepared by purification of RNA on oligo dT Cellulose, using the instructions for Poly (A) Pure mRNA isolation kit (Ambion Inc., Austin, TX).

The RT-PCR was conducted as described by Perkin Elmer LTD protocols. Several sets of primers were designed from the sequence of the MAG gene, examples of which are shown in Table 4 below.

Table 4: MAG Gene Primer Examples

Fragment Base Pairs Location Sequence Number

1 104 upstream 5'AAGTTATATTAGAATCGTGTC3' SEQ. ID NO: 5 2 downstream 5'CTTGATGCAAAGTCGGTGCTC3' SEQ.ID NO:10

3 127 upstream 5'GGACTTGATTCCTTCATTCAGTC3' SEQ. ID NO: 11

4 downstream 5'CTCCTCTACTATATAAGCTCTGA3' SEQ.ID NO: 12

The rapid amplification of cDNA ends-polymerase chain reaction (3' RACE-PCR) was carried out according to 573' RACE kit (Boehringer Mannheim, Indianapolis, IN) protocol. 3' RACE takes advantage of the natural poly (A) tail of mRNAs as a priming site for PCR amplification. First-strand cDNA synthesis was initiated at the poly(A) tail of mRNA using the oligo d(T) anchor primer. After converting mRNA into cDNA, the following amplification is then direcdy performed without a further purification step using the PCR oligo d(T) anchor primers SEQ. ID NO: 13 and 14 shown in Table 5 below.

Table 5: PCR Oligo Anchor Primers

SEQ. ID NO: 13 5'GACCACGCGTATCGATGTCGACTTTTTTTTTTTTTTTTV 3'

SEQ. ID NO: 14 5'CCAGCTTTGGCCAGCTTACTAT3' * _* User designed specific primer.

The 3'RACE PCR analysis of MAG gene yielded a 536 bp product in HCV cirrhotic liver (lane 4), macroregenerative nodule (MRN, lane 6), and HCC (lane 5), but not in normal donor liver (lane 3) and placenta (not shown) in the same experiment. 3 'RACE PCR was performed twice separately with identical results. Lanes 1 and 2, 100 bp and 1 kb DNA ladders. The 536 bp 3'RACE-PCR fragment was cloned into the Sma I site of pGEM 3Zf (+) plasmid (Promega #). Antisense 276 bp probe was obtained by digesting 536 bp probe, according to the restriction map.

The RNA dot blot analysis was conducted as follows. RNA was transferred to nylon membranes (Schleicher & Schuell, Keene, NH) by using a Bio-Rad (Richmond, VA) dot-blotting apparatus. RNA was fixed onto the membrane by short-wave UV irradiation using Stratalinker (Stratagene, La Jolla, CA) for 40 sec. Membranes were pre-hybridized for 4 h at 42^CC in 50% deionized formamide, 7% sodium dodecyl sulfate (SDS), 10% bovine serum albumin, 1 mM EDTA and 0.2 M sodium phosphate pH 7.2. The 536 bp cDNA human MAG probe was radiolabeled with ³²P by random primer oligolabeling in the presence of [(³²P]-dCTP. Membranes were hybridized at 42°C for 20 hrs.

The transcription reaction was conducted as follows. A 276 bp fragment of MAG gene cloned in pGEM 3Zf(+) was used to prepare the antisense probe. To this end, 2 μg of DNA template were used along with lOx transcription buffer with DDT, a mixture of nucleotide 1 μl of each (ATP, CTP, GTP-10 mM), 5 μl of labeled UTP-10 mM, 2 μl of T7 RNA polymerase - ribonuclease inliibitor (Ambion Inc. Austin, TX) in a total volume of 20 μl, after incubation 1 μl of RNase-free DNase I (2U/μl) were added to the reaction for 15 min. at 37°C. See, Sambrook, J., Fritsch E. F., and Maniatis, T. , Molecular cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, cold Spring Harbor, NY (1989).

The ribonuclease protection assay (RPA) was conducted as follows. RPA II Itit (Ambion Inc. , Austin, TX) was used according to the commercial protocol. Briefly, poly(A) pure RNA (1 μg for each sample) was hybridized with 2xl0⁶ cpm of ³²P-UTP labeled antisense probe and incubated overnight at 42°C. Equivalent amounts of total yeast RNA and yeast tRNA were set up as controls for the probes to be used. 200 μl of concentrated RNase A/RNase TI mixtore in RNase digestion buffer (1:50) was added to all experimental tubes, and to one tube of each pair of yeast RNA of control tubes. To the remaining yeast .RNA control tubes, only 200 μl of RNase digestion buffer without RNase was added and incubated during 20 min. at 37°C. Samples were analyzed on 5% polyacrylamide/lx TBE gels 4- 8M urea, followed by autoradiography. The protected probe was 276 bp long, and the unprotected probe, 290 bp long. Example 11: DNA and Protein Sequences

When studying the expression of the c-met proto-oncogene in normal and neoplastic human liver by reverse transcription-polymerase chain reaction (RT-PCR), primers specific for c-met were used. See, Ljubimova J.Y., et al.., Digest. Dis. Sci. 42:1675-1680 (1997); Ljubimova et al., Histochem. & Cytochem. 45: 79 (1997). In cirrhotic and HCC livers, an extra PCR band of approximately 150 bp was consistently observed. This band very likely is an alternatively spliced variant of c-met or a novel human gene amplified under low stringency conditions. This band was cut from the gel, sequenced (only a short stretch of sequence homology with c-met was revealed) and specific primers for RT-PCR prepared. Using 3 'RACE PCR analysis, a larger cDNA fragment of 536 bp was obtained, which overlaps the original 154 bp fragment. The complete cDNA sequence (569 bp) is shown in Table 6 below. Table 6: Polynucleotide Sequence

TGGTCCTTTG GCGTCGTCCT CAAGTTATAT TAGAATCGTG TCCTCCCGGC TTTGGCC.AAC TTACTATTCT

AGGACTTGAT TCCTTCATTC AGTCACAATT TATTGAGCAC CGACTTTGCA TCAACCTCTT GCTGAAGATA

ACAGTGCTGA CAATATACAG CCCTGCCCTC AGAGCTTATA TAGTAGAGGA GAAAAAGTGA ACCCATAATA TACAGTCAGT AGCGAGTATT TACTAAGTAC TTTCTATTTG CGAGGCCCTG ATAAAAGTAC TGTCCTGGCC

AGGCGCGGTG GCTCACGCCT GTAATTCCAG CACTTTGGGA GGTCGAGGTG GGCAGATCAC CTAAGGTCAG

GAGTTCGAGA TCAGCCTGGC TAACATGGGG AAACCCCGTC TCTACTAAAA ATGGAAAAAT TAGCTGGGCA TGGTGGCGGG CGCCTGT.AAT CCCAGCTACT CGGGAGGCTG AGACAGGAGA ATGACTTGAA CCCAGGAGTT GCAGTGGCCA AGATAAGATA GCGCCATTGT ACTCCAGCCT GGGTAACACA GCGAGACTGT GTCTCAAAAA AAAAAAAAA (SEQ. ID NO: 7)

This sequence has a high degree of homology (95%) with a minus strand stretch of a genomic sequence of the "ERCC2 gene cluster" outside of genes ERCC2, C and KLC2. See, Lamerdin JE, et al., Genomics 34:399-409 (1996). The 569 bp DNA fragment sequence, however, was located outside of all these three genes and clearly represents at least a portion of the gene. Using specific primers for the 104 bp DNA sequence within this fragment (outside of short c-met homology region), the expression of the gene was studied in 18 human fresh-frozen samples of human liver tissues by RT-PCR: 4 normal livers, 1 fulminant liver, 7 cirrhotic livers (2 with small HCC nodules), and 6 HCCs. No expression of the gene was detected in 4 normal and 1 fulminant failure liver. In contrast, the expression of this gene was detected in all cirrhotic and 5 of 6 HCC livers.

An analysis of the gene sequence revealed that the 154 bp DNA sequence contains an open reading frame as shown in Table 6 above. An amino acids comparison of the protein sequences encoded by the a) 154 bp DNA fragment and the b) 536 bp (3 'RACE) DNA fragment is shown in Table 7 below. An overlap over a large number of amino acids evidences that the DNA segments encode the protein. This suggests that it is likely codes for the protein.

Table 7: Deduced Fragment Protein Sequences a) VL RRPQVILESCPPΞFGQLTILGLDSFIQSQFIEHRLCIKLLLKITLMM (SEQ. ID NO: 8) b) PSPPGFGQ TILGLDCFIQSQFIEHRLCI LLLKITVLTIYSPALRAYIVEEKK*

(SEQ. ID NO:9) * position of stop codon

Boldface: identical residues in a) and b).

Example 12: Gene Expression in Other Tissues

A study was carried out by RT-PCR to determine which tissues, other than liver, express the novel gene. This study was conducted with the aid of primers for the 104 bp DNA fragment. Samples from various human tissues, including additional liver samples were utilized, to a total of 55 tissues where 30 were liver samples of different etiologies.

The gene was found to be expressed in 16 of 16 advanced liver cirrhoses of viral etiology

(6 HBV and 10 HCV), 8 of 10 HCC, 1 of 1 leukemic spleen, 1 of 2 breast carcinomas, 1 of 2 endometrial carcinomas and a metastasis of the positive one, 3 of 3 ovarian carcinomas, 3 of 4 colon carcinomas and 1 of 1 surrounding tissue, 1 of 1 prostate, 1 of 1 lung, 1 of 1 renal and 1 of 1 uterine carcinomas. Eleven out of 11 normal tissues, i.e., placenta, spleen, gall bladder, fallopian tube and liver, were found not to express the gene. Six tissue samples from patients afflicted with fulminant liver were also found not to express this gene as is shown in Table 8 below. Table 8; Expression of MAG Gene in Normal and Diseased Human Tissues

As a necessary control, it was confirmed that in tumors, other than liver tumors, the obtained PCR product was indeed the novel gene fragment. The corresponding PCR bands from several randomly chosen tumors were sequenced, and the sequences were found to be identical to that of the 104 bp gene fragment. The present gene is thus referred to as "malignancy associated gene" (MAG), on the basis of the expression of the novel gene in malignant tumors but not in normal human tissues. Example 13: mRNA and Expression of MAG Gene Product

The 536 bp 3'RACE fragment was used for RNA dot blot analysis. For the RNA dot blot analysis of the expression of a novel gene in normal and malignant human tissues, RNA was extracted from normal tissues (1 liver, 1 placenta, 2 gall bladders), 1 HCC and 1 MRN with dysplasia from the same patient,

1 endometrial carcinoma and 1 metastasis from the same patient; 2 HCV cirrhotic livers, 1 lung, 1 colon, 2 ovarian, 1 prostate, 1 uterine carcinomas; 1 colon and 1 colon carcinoma surrounding tissue.

Positive signals were detected in 9 out of 13 malignant tissues and 1 colon carcinoma surrounding tissue, whereas none of the normal tissue samples (placenta, liver and 2 gall bladders) demonstrated the expression of MAG gene.

To obtain evidence of MAG gene expression at the mRNA level, the Ribonuclease Protection Assay (RPA) method was used on poly(A) mRNA from normal donor liver, two human liver tumor tissue cultures, Hep3B and Hep G2, a colon cancer and an ovarian cancer. The probe was protected from RNase digestion (positive MAG gene expression) in ovarian cancer and HepG2 cells, in contrast to normal liver, colon cancer and Hep3B cell culture, that were also all negative for MAG gene expression by RT-PCR. The RPA results were thus in complete agreement with RT-PCR data on the same mRNA samples (data not shown).

The GenBank Accession No. for the MAG sequence is AF041410. The present human malignancy-associated gene (MAG) is expressed in various malignant tumors including glioblastomas and hepatocellular carcinomas (HCC), as well as in tumor pre-existing conditions such as hepatitis C virus- and hepatitis B virus-induced liver cirrhosis. The expression of MAG was characterized using reverse transcription polymerase chain reaction (RT-PCR), rapid amplification of cDNA ends (3 'RACE) PCR, RNA dot blotting, ribonuclease protection assay (RPA) and Northern blot analysis. 3'RACE PCR yielded a 536 bp MAG fragment in HCC, macroregenerative liver nodules with dysplasia and liver cirrhosis but not in normal liver or placenta. By RT-PCR, MAG expression was found in none of 12 different normal tissues but found in 46 of 51 (90%) premalignant and malignant tissues of various sites. Embryonic liver and brain were found to be positive for MAG expression together with tumors from the same organs, but the corresponding normal adult tissues were negative. By RPA, MAG mRNA was expressed in the HepG2 liver tumor cell line and in an ovarian carcinoma but not in normal liver. The estimated transcript size from Northern blot analysis was 8.8 kb. This novel gene may play a role in the progression of premalignant conditions and in the development of HCC and other cancers.

EXTENSION OF NUCLEIC ACID SEQUENCE Example 14: Materials Utilized Fresh-frozen human tissues (a total of 69 samples) not used for diagnosis purposes were obtained from the Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA.

Cultures of human tumor hepatocyte cell lines, HepG2 and Hep3B were obtained from the American Type

Culture Collection (ATCC), Rockville Pike, MD, and were propagated according to the ATCC protocol. A ltit for determining total RNA was purchased from Clontech Laboratories (Palo Alto, CA), and utilized for determining total mRNA from human adult brain, embryonic liver and embryonic brain.

Example 15: Nucleic Acid Sequencing

Nucleic acids equencing was carried out as described by Sanger et al. Sanger, F., Nicklen, S.,

Coulson, A.R., DNA sequencing with chain-terminating inhibitors, P. N. A. S. (USA) 74: 5463-5467 (1977).

The Sequenase ltit included Sequenase DNA polymerase (United States Biochemical, Cleveland, OH). ³⁵S- dATP was obtained from Amersham (Arlington Heights, IL). Sequencing gels were run on an IBI Standard

Sequencer STS 45 (New Haven, CT). cDNA fragments subcloned in pGEM 3Zf(+) plasmids were prepared for sequencing according to the Promega Biotech (Madison, WI) commercial protocol.

Example 16: Preparation of tissue mRNA

Total RNA (50-100 (g) was isolated as described by Chomczynski and Sacchi, with modification (15), using TRIzol reagent (Life Technologies, Gaithersburg, MD). Chomczynski, P. and Sacchi, N.,

Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction, Anal.

Biochem. 162: 156-159 (1987). The tissue was homogenized in TRIzol solution at 4oC (1 ml TIUzol per 100 mg tissue). After 5 min. incubation at room temperature, 0.2 ml chloroform was added per 1 ml TRIzol.

RNA pellets were washed with 75% ethanol, air dried and treated with 20 U RNase-free DNase (Ambion Inc., Austin, TX). The OD260/OD280 ratio was determined spectrophotometrically for RNA quantitation.

Poly(A)-containing RNA was prepared by purification of RNA on oligo dT cellulose, using the Poly

(A) Pure mRNA isolation kit (Ambion Inc.).

A Dnase/RNase treatment of the RNA was performed by digesting total RNA for 1 hr at 370C, using 20 U of either DNase or RNase. Both enzymes were purchased from Ambion Inc. Reverse transcription-polymerase chain reaction (RT-PCR) was carried out as previously described by Ljubimova et al (1997a and b). Ljubimova, J.Y., Pet al., Expression of HGF, its receptor c-met, c-myc, and albumin in cirrhotic and neoplastic human liver tissue, J. Histochem Cytochem. 45: 79-87 (1997a);

Ljubimova, J.Y., et al., Lack of hepatocyte growth factor receptor (c-met) gene expression in fulminant hepatic failure livers before transplantation. Digest, Dis. Sci. 42: 1675-1680 (1997b). From the novel gene sequence, several sets of primers were designed for fragments of different sizes. The sequences of these promers are shown in Table _ below. Table 9: Primer Sequences

Fragment Forward Primer SEQ. ID NO: Reverse Primer SEQ. ID NO:

(5' to 3') (5' to 3')

104 bp AAGTTATATTAGAATCGTGTC 15 CTTGATGCAAAGTCGGTGCTC 16 127 bp GGACTTGATTCCTTCATTCAGTC 17 CTCCTCTACTATATAAGCTCTGA 18

Routine negative controls (without reverse transcriptase and a water control), and a positive kit control were included in each reaction.

Rapid amplification of cDNA ends-polymerase chain reaction (3' RACE PCR) was carried out using 573' RACE kit (Boeliringer Mannheim, Indianapolis, IN). 3' RACE takes advantage of the natural poly(A)+ tail of mRNAs as a priming site for PCR amplification. First-strand cDNA synthesis is initiated at the poly(A)+ tail of mRNA using the oligo d(T) anchor primer. After converting mRNA into cDNA, the following amplification was directly performed without a further purification step using the PCR oligo d(T) anchor primer and MAG-specific primer shown in Table 10 below. Table 10: Primers Used

Anchor Primer 5 ' -GACCACGCGTATCGATGTCGACTTTTTTTTTTTTTTTTV-3 ' (SEQ. ID NO:19) MAG-specific Primer 5 ' -CCAGCTTTGGCCAGCTTACTAT-3 ' (SEQ. ID NO:20)

Example 17: RNA Dot Blot analysis

The 536 bp 3'RACE PCR fragment was cloned into the Sma I site of pGEM 3Zf(+) plasmid (Promega Biotech) and used as a random primed probe. Total tissue RNA was transferred to nylon membranes (Schleicher & Schuell, Keene, NH) using a

Bio-Rad (Richmond, VA) dot-blotting apparatus. RNA was fixed onto the membrane by short-wave UV irradiation using Stratalinker (Stratagene, La Jolla, CA) for 40 sec. Membranes were pre-hybridized for 4 h at 42oC in 50% deionized formamide, 7% sodium dodecyl sulfate (SDS), 10% bovine serum albumin, 1 mM EDTA and 0.2 M sodium phosphate pH 1.2. The 536 bp cDNA human MAG probe was radiolabeled by random primer oligolabeling in the presence of [(32P]dCTP. A nick-translated probe (a total of 5xl0⁶ cpm) was used in the hybridization solution. Membranes were hybridized at 42oC for 20 h. Example 18: Transcription Reaction

A 276 bp fragment of MAG gene cloned in pGEM 3Zf(+) was used to prepare the antisense probe. An anti-sense 276 bp probe was obtained by digesting the 536 bp probe, according to the restriction map. Two μg of DNA template, lOx transcription buffer with DDT, a mixtore of nucleotides containing 1 μl of each (ATP, CTP, GTP, all 10 mM), 5 μl of 10 mM solution of labeled ³²P-UTP (a total of 5x106 cpm), 2 μl of T7 RNA polymerase + RNase inhibitor (Ambion Inc.), in a total volume of 20 μl were used. After incubation, 1 μl of RNase-free DNase I (2 U/μl) was added to the reaction for 15 min. at 37oC as described by Sambrook et al. Sambrook, J., et al, Molecular Cloning: a Laboratory Manual, Cold Spring Harbor: Cold Spring Harbor Laboratory Press (1989). Example 19: Ribonuclease Protection Assay (RPA) An RPA II kit (Ambion Inc.) was used according to the supplied protocol. Briefly, poly(A)+ pure

RNA (1 (g for each sample) was hybridized with 2x106 cpm of ³²P-UTP labeled antisense probe and incubated overnight at 420C. Equivalent amounts of total yeast RNA and yeast tRNA were set up as controls for the probes to be used. 200 μl concentrated RNase .A/RNase TI mixture in RNase digestion buffer (1:50) was added to all experimental tubes, and to one tube of each pair of yeast RNA of control tobes. To the remaining yeast RNA control tobes, only 200 μl of RNase digestion buffer without RNase was added and incubated for 20 min. at 37oC. Samples were analyzed on 5% polyacrylamide/lX TBE gels with 8 M urea, followed by autoradiography. The size of a protected probe was 276 bp, and of the unprotected probe, 290 bp. Example 20: Northern Analysis Hybond N membrane (Amersham Life Science Inc.) was pre-hybridized for 14 h at 42oC in 50% deionized formamide, 1 % SDS, 5xSSPE, 2xDenhardt's and 10 mg/ml tRNA. The 536 bp cDNA to human MAG was radiolabeled by random primer oligolabeling in the presence of ³²P-dCTP. The membranes were washed in 2xSSPE, 0.1 % SDS at room temperature two times for 10 min., then in lxSSPE, 0.1 % SDS at 650C for 15 min. and in 0.1 SSPE, 0.1 % SDS at 65oC for 10 min. Membranes were exposed to pre-flashed Kodak XAR-5 film at -70oC for 2 days. As a control, we used β-actin cDNA (Life Technologies) labeled as described for MAG. After hybridization with a MAG-specific probe, the same blot was stripped and reprobed for β-actin as described by Ausubel et al. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, R.E., Seidman, J.G., Smith, J.A., Struhl, K., Eds., Current Protocols in Molecular Biology, New York: J. Wiley & Sons (1987). All samples were positive for (-actin. Hybridization and washing were done exactly as for MAG treatment. Membranes were autoradiographed at -70oC overnight.

Example 21: Results and Comments

When studying the expression of the c-met proto-oncogene in normal and neoplastic human liver by RT-PCR, primers specific for c-met were employed as described by Ljubimova et al. Ljubimova, J.Y., et al., Digest. Dis. Sci. 42: 1675-1680 (1997). An extra PCR band of approximately 150 bp was consistently observed in cirrhotic and HCC livers, but not in normal liver. This band likely represents an alternatively spliced variant of c-met or a novel human gene amplified under low stringency conditions. The band was cut from the gel and sequenced, and it was found that the 154 bp sequenced RT-PCR fragment contained a short stretch of sequence homology with c-met. Specific primers for RT-PCR analysis of the novel gene were then designed, in the area on a sequence map between the c-met primers. A larger cDNA fragment of 536 bp, partially overlapping the original 154 bp fragment, was obtained using 3 'RACE PCR analysis. 3 'RACE PCR yielded a 536 bp product in hepatitis C virus cirrhotic liver, HCC and liver macroregenerative nodules with dysplasia, but not in normal placenta or normal adult donor liver in the same expeiiment. A run with MAG analysis by 3' RACE PCR yielded a 536 bp product in hepatitis C virus cirrhotic liver , HCC and macroregenerative nodule, but not in normal donor liver in the same experiment. A 100 bp DNA ladder obtained from Life Technologies was run concurrently in a separate lane (data not shown). 3 'RACE PCR was performed twice and the results obtained were the same. The complete sequence of the 569 bp cDNA , obtained based on the alignment of 154 bp and 536 bp fragments, is shown in Table _ below. Sequence analysis revealed that the entire 154 bp sequence contained an open reading frame encoding the amino acid sequence shown in the same table. The data show that the gene actually codes for a real protein.

RT-PCR with specific primers for the 104 bp sequence within this fragment (outside of a short c-met homology region) was used to study the expression of the gene in 18 human fresh-frozen samples of explanted human liver tissues by RT-PCR. These samples included 4 normal livers, 1 fulminant hepatic failure liver, 7 cirrhotic livers (2 with small HCC nodules) and 6 HCCs. No expression of the novel gene was detected in the 4 normal livers and 1 fulminant hepatic failure liver. In contrast, the expression of this gene was detected in all cirrhotic livers and in 5 of 6 HCCs (Data not shown). Another set of novel gene-specific primers for a 127 bp product, was designed to test normal adult and fetal brain and liver, and 4 glioblastomas. All glioblastomas (1 grade III and 3 grade IV) were found to contain the fragment, that is they were positive for the gene, while normal adult brain did not. Fetal liver and brain were compared for MAG expression with noimal adult liver and brain, and with tomors of the same organs. Normal adult liver and brain were found not to contain the fragment (negative for MAG expression), but embryonic and malignant liver and brain tissues did express the gene.

In the second series of RT-PCR studies of normal and diseased human tissues, the expression of the present gene was found in the vast majority of malignant and premalignant tissues but not in normal or non-tumor (fulminant hepatic failure livers) tissues as shown in Table 9 below.

Table 9: Expression of Novel MAG Gene in Normal and Diseased Human Tissues revealed by RT-PCR Tissue Type No.Samples Total No. w/Expression

Normal

Liver 0 4

Gall bladder 0 2 Placenta 0 2

Fallopian tube 0 1

Kidney 0 1

Brain 0 1

Spleen 0 1 Non-tumorous

Fulminant hepatic failure liver

Tumor and premalignant

Cirrhotic liver 16 16 (6 HBV + 10 HCV)a

Liver macroregenerative 2 2 nodules

Hepatocellular 10 carcinoma Meningioma 1 1

Glioblastoma 4 4

(grades III and IV)

Lung carcinoma 1 1

Breast carcinoma 1 2 Leukemic spleen 1 1

Renal carcinoma 1 1

Colon carcinoma 3 4

Tissue surrounding 1 1 colon carcinomac Prostate carcinoma 1

Ovarian carcinoma 3

Uterine carcinoma 1

Endometrial carcinoma 2

Metastasis of 1 endometrial carcinoma a - HBV, hepatitis B vims; HCV hepatitis C vims b - one sample with dysplasia c - from a patient witn MAG-p poossiittiivvee p prriimmaarryy ttuurmror

The fact that the RT-PCR product obtained in tumors other than liver tumors was indeed a novel gene fragment was confirmed, as a necessary control. The corresponding PCR band from several randomly chosen tomors was sequenced, and the sequence was found to be identical to that of the 104 bp novel gene fragment.

The 536 bp 3 'RACE PCR fragment was used as a probe for dot blot analysis of RNA extracted from 4 normal tissues and 16 tumor and premalignant tissues. An RNA dot blot analysis of ethe expression of the present in normal and malignant human tissues showed that normal liver, placenta and gall bladder tissues lacked the fragment, whereas HCC, macroregenerative liver nodule with dysplasia and a metastasis of endometrial carcinoma did. Moreover, HCV cirrhotic livers, lung carcinoma, and colon carcinoma tissues did have the fragment. Although initially prostate carcinoma, ovarian carcinoma and uterine carcinoma tissues did not evidenced the presence of the fragment a more sensitive RT-PCR revealed MAG expression in all these cases. Each sample had a corresponding blank which did not contain the fragment, a control with colon carcinoma which did show the fragment, and a control with tissue surrounding colon carcinoma from the same patient which did not contain the fragment (data not shown).

Positive signals were detected in 9 of 16 malignant and premalignant conditions, that is HCC, macroregenerative liver nodule with dysplasia, metastasis of an endometrial carcinoma, two hepatitis C liver cirrhoses, carcinomas of the lung, colon, ovary (one of two) and a colon carcinoma surrounding tissue.

Furthermore, none of the normal tissue samples, including liver, placenta, and two gall bladder samples demonstrated the presence of the fragment, e. i. MAG expression.

Three approaches were further used to conclusive prove MAG gene expression at the mRNA level. First, polyA+ mRNA from normal adult donor liver, an ovarian carcinoma, an HCC, and a HepG2 cultured human liver tumor cell line were studied by RT-PCR. The MAG-specific band was observed only in tumor samples, but not in the normal tissue samples. Second, total RNA was treated with DNase or RNase before being analyzed by RT-PCR for MAG expression. The MAG RT-PCR band could be seen after DNase treatment but not after RNase treatment. These data confirm that the 127 bp MAG band is amplified from mRNA but not from residual cellular DNA.

In yet a third approach, the RPA method was used on polyA+ mRNA from normal adult donor liver, an ovarian carcinoma, a colon carcinoma, and two cultured human liver tumor cell lines, HepG2 and Hep3B. In ovarian carcinoma and HepG2 cells, the probe was protected from RNase digestion (positive MAG mRNA expression)(data not shown). In contrast, normal liver, colon carcinoma and Hep3B cells were all negative for MAG expression by RT-PCR (data not shown). The RPA results were thus in complete agreement with RT-PCR data on the same mRNA samples.

Northern analysis was used to screen several tissues for MAG expression with the 536 bp cDNA fragment as a probe, and determine the MAG transcript size. A positive signal was observed in cirrhotic liver and HCC but not in normal liver and placenta (data not shown). The estimated size of the corresponding mRNA was 8.8 kb.

The above data present a partial characterization of a gene expressed in various human tumors and pre-malignant conditions but not in normal tissues. A 154 bp MAG fragment was initially obtained in RT-PCR experiments involving c-met proto-oncogene with which it shares a short region of homology. Subsequently, 3'RACE PCR allowed the extension of its sequence to 569 bp. More recently, a genomic sequence of the human ERCC2 gene and of two adjacent genes, C and KLC2, referred to as the ERCC2 gene cluster, appeared in the GenBank. See, Lamerdin, J.E., et al., Sequence analysis of the ERCC2 gene regions in human, mouse and hamster reveals three linked genes, Genomics 34: 399-409 (1996). A comparison of the sequences of the gene of this invention and the gene cluster obtained from the GenBank revealed a minus strand stretch in the ERCC2 cluster, which has 95% sequence similarity with the 569 bp fragment of the present invention. This stretch is located within a 3' 12 kb region of the ERCC2 gene cluster 54 kb genomic sequence. Since the sequence homologous to present nuclaic acid lies outside of all fhree genes in this cluster, the present gene in all likelihood is a different and novel gene. Moreover, 3 'RACE PCR yielded a continuous sequence of the new gene from the initial fragment down to the polyA tail that is most likely the mRNA for the gene of this invention.

Several methods were used to establish more rigorously that the present gene is really expressed at the mRNA level and that it is not artifactually amplified from residual DNA present in the RNA preparations. All of the following techniques confirmed the existence of the mRNA of the present gene. (1) RNA samples were pre-treated with RNase-free DNase and DNase-free RNase before RT-PCR. After DNase treatment of RNA samples, an usual MAG band was obtained but after RNase treatment no band could be found. (2) Northern blot analysis of several tissues evidenced a single band of about 8.8 kb in tomor but not in normal tissue, in full agreement with the data obtained by RT-PCR.

(3) RPA analysis of mRNA from normal and tomor tissues and cultures showed specific protection from RNase digestion of the sequence of the present gene in tomor but not in normal tissues.

Taken together, the above data strongly support that the expression of the present gene at the mRNA level, and that this expression is specific to tomors and to pre-malignant conditions.

5 'RACE PCR was performed to extend the 569 bp cDNA MAG fragment in the 5' prime direction. This attempt, however, was unsuccessful. This may be due to a large transcript size of MAG that precluded its full-length amplification by 5' RACE PCR. The RT-PCR analysis of large number of samples from human tumors and tomor pre-existing conditions (such as liver cirrhosis and macroregenerative nodules) has shown a striking and clear difference between lack of expression in normal tissues and positive expression in most premalignant and malignant tissues. The expression of the present gene, originally found in liver tissue only, has now been detected by the inventors not only in liver cirrhosis, pre-malignant macroregenerative nodules with dysplasia and HCC, but in various other human malignancies including glioblastomas and carcinomas of the lung, breast, colon, kidney, prostate, endometrium, ovary and uterus. This is similar to the pattern evidenced by other genes where there is specific tomor gene expression. See, Ross, J.S., et al., HER-2 neu gene amplification status in prostate cancer by fluorescence in situ hybridization, Hum Pathol. 28: 827-833 (1997). For instance, prostate specific antigen expression is a reliable biomarker for prostate cancer. However, the expression of this antigen is also found in breast cancer. See, Diamandis, E.P., et al., Non- prostatic sources of prostate-specific antigen, Urol Clin North Am. 24: 275-282 (1997). Moreover, the HER-2/neu gene, a biomarker for breast cancer, was amplified in non-diploid prostate cancers, but not in diploid prostate cancers. See, Cioce, V., et al., Hepatocyte growth factor (HGF)/NK1 is a naturally occurring

HGF/Scatter factor variant with partial agonist/antagonist activity, J. Biol. Chem. 271 : 13110-13115 (1996).

In order to determine whether MAG belongs to the group of oncofetal genes, the present story was extended to analyzed the gene's expression in normal embryonic human liver and brain. Damjanov, I. Teratocarcinoma: Neoplastic lessons about normal embryogenesis. Int J Dev Biol., 37: 39-46, 1993. The results demonstrate that the MAG gene is expressed in fetal and malignant liver and brain tissues but is not expressed in corresponding adult normal tissues. The present data regarding MAG expression in fetal and malignant tissues vs. adult normal tissues agree with the data on the expression of embryonic genes in some tumors. Examples includethe expression of α-fetoprotein in both embryonic liver and HCC (24,25), and midkine, a neurotrophic and angiogenic growth factor, which is produced in fetal and malignant astrocytes but not in normal adult astrocyte. Yen, Y.-C, et al., Cancer Res. 47: 896-901 (1987); Carr, B.I., et al., In: Primary Liver Cancer: Etiological and Progression Factors, C. Brechot, ed., pp.249-268, Boca Raton: CRC Press (1994); Mishima, K., et al., Neurosci Lett. 12: 29-32 (1997).

It has been shown that human fetal brain and malignant glial tumors express monocyte chemoattractant protein-1 (MCP-1) in vivo and in vitro but normal adult brain does not. See, Desbaillets, I., et al., Int. J. Cancer 58: 240-247 (1994). The analysis of 30 liver and 5 brain disease cases for MAG expression has indicated its potential importance in liver and brain neoplasia. The absence of MAG expression in different normal tissues and its presence in various malignancies supports the important role of the present gene in malignant cell transformation. Most recently, the inventors have established a tissue culture system to study MAG expression and its regulation involving hepatic HepG2 and Hep3B tumor cell lines. MAG expression was detected by RT-PCR and RPA only in the HepG2 cell line, and its expression was shown to be inhibited in HepG2 cells by factors important for liver and other tissue growth, hepatocyte growth factor (10 ng/ml, 48 h.) and transforming growth factor-βl (1.5 ng/ml, 48 h.).

In summary, we have partially characterized a novel human gene, the malignancy-associated gene or MAG. This gene is expressed at the mRNA level in malignant and pre-malignant tissues obtained from various body locations, but not in the various normal tissues tested. This gene is an oncofetal gene as defined by Damjanov, given that it is additionally expressed in fetal tissues such as fetal liver and brain, and has an important role in embryogenesis and tomor development. See, Damjanov I., Int J Dev Biol. 37: 39-46 (1993). Example 22: Screening of HepG2 cDNA Library for Extension of DNA Sequence

The instruction manual of Clontech Hep G2 cDNA Library were followed for all work with DNA libraries, with few modifications. The present DNA library was plated in triplicate onto NZY agar using the following dilutions: 1 X 10⁷ plaque forming units (pfu) per 150 mm plate, 3.33 x 10⁶ pfu, 1.11 x 10⁶pfu, 3.1 x 10⁵ pfu, 1.23 x 10⁵ pfu, 4.1 x 10" pfu, and 1.3 x 10⁴ pfu per plate, a threefold set of dilutions, or about 4.5 x 10⁷ pfu/probe. After overnight incubation at 37°C, the phages were lifted onto Hybond N filters (Amersham Life Sciences) in duplicate, denatured, neutralized and rinsed as per protocol, and the filters vacuum dried at 80°C.

Labeling, pre-hybridization and hybridization were conducted in accordance with the two following methods.

(1) A gene specific 34-mer probe end-labeled with γ³²P dATP was used. 100 pmole of the oligo were incubated with 10 mi of 150 mCi/mole label, 3 ml 10 x buffer, 45 units Stratagene T4 polynucleotide kinase in a total volume of 30 ml. The reaction mixtore was then incubated for 60 min. at37°C, and stopped with 1 ml of 0.5 M EDTA. The unincorporated label was removed with a Bio-Spin 6 column (Bio-Rad, Richmond, VA).

(2) Approximately 5.5 x 10⁵ counts/ml of a gene specific probe were used, which was a PCR product of the 3 '-RACE fragment consisting of the region between the SP6 site of pGEm vector (Promega) and the spl-5 site on the 3 'RACE fragment of 180 bp. This probe was random-primed with α-dCTP following the Boehringer Mannheim protocol, and cleaned up with Boehringer Mannheim Quick Spin Sephadex G-509 columns.

The prehybridization and hybridization were conducted as indicated in the Stratagene manual. The filters were pre-hybridized for 2 hrs at 65°C with the same prehybridization solution utilized for the oligo probe, which contained 6 x SSC, 20 mM NaH₂P0₄, 0.4% SDS, 5xDenhardt's reagent and 500 μg/ml denatured sonicated salmon sperm DNA. The hybridization solution utilized for the oligo probe was the same as that used for pre-hybridization, but without the Denhardt's solution. The filters were hybridized overnight at 65°C and washed in 6xSSC, 0.1 % SDS under the following conditions: room temperature, 30 min; 45°C, 45 min; 55°C, 45 min; 60°C, 45 min. twice. The random primed probe was pre-hybridized in 2xPipes Buffer, 50% deionized formamide, 0.5% SD, and 100 mg/ml salmon speπn DNA for 2 hrs. at 42°C, and hybridized in the same solution overnight at 42°C. The random-primed probe was washed with 0.1 % SSC, 0.1 % SDS for 1 hr. at 50°C, and for 1 hr. at 65°C. Example 23: Hep G2 cDNA Library Clone Identification & DNA Isolation

One colony of each respective isolate was grown in Luria-Bertani broth with 50 μg/ml of ampicillin. The DNA was isolated via a modified alkaline lysis procedure, followed by the binding of the DNA to a Qiagen anion-exchange resin in low salt (Qiagen, Chatsworth, CA). Briefly, the bacteria are resuspended in 50 mM Tris-HCl, pH 8.0, also containing 10 mM EDTA, 100 μg/ml RNase A, lysed with 200 mM NaOH and 1 % SDS, and neutralized in 3.0 M potassium acetate, pH 5.5. The DNA was then equilibrated in a solution containing 750 mM NaCl; 50 mM MOPS, pH 7.0; 15 % ethanol and 0.15 % Triton X-100, washed with 1.0 M NaCl; 50 mM Tris-HCl, pH 8.5; 15% ethanol, and eluted in 1.25 M NaCl; 50 mM Tris-HCl pH 8.5; 15% ethanol. The resulting pellets are dried and resuspended in TE (10 mM Tris-HCl, pH 8.0, 1 mM EDTA). Example 24: Identification of Clones by PCR Amplification & Southern Analysis

To determine the insert size of these clones, the obtained nucleic acid (DNA) was PCR-amplified with SP6 and T7 primers under the following conditions: 95°C 3 min, 35 cycles (each cycle was: 94°C-30 sec, 60°C-45 sec, 72° C 30 sec), and 3 min at 72°C with 1.5 mM of MgCl₂ in 100 μl of a total volume. A Perltin Elmer (Brunchburg, NJ) DNA Kit was used for this study.

To verify that these clones contained the DNA of interest, the amplified products were subjected to Southern analysis. The PCR products were resolved through a 1 % agarose gel for 2 hr at 80 V and denatured in 0.25 M NaOH for 15 min. The DNA gel is transferred to Zeta-Probe blotting Membrane (Bio-Rad Laboratories, Richmond, CA) with a Hoefer Transphor apparatus (Hoefer Scientific Instruments, San Francisco, CA) in 25 mM Na₃P0₄ for 2 lirs at 1.0 A at 4°C. The membranes were prehybridized in 2xPIPES, 50% deionized foπnamide, 0.5% SDS, and 100 μg/ml denatured sonicated salmon sperm DNA for 2 hrs. at 42°C, and then hybridized according to the conditions for oligo and random-primed probes, as described in the screening procedure. The Southern blot revealed that all clones contained the following 373 nucleotide DNA insert.

Table 10: Extension to MAG DNA Sequence

5'-GGGGATTGTA G.AAATATGGG CAAGTACCAT ATTGTAAAGG GTATCCTGTG AGATGTGTTG

AGAATACAGG CTTTATACTC TGGGAGACTG TGAAGCCACT AAATAGAAGA GTGACTTAGG TTACACTATC TAACTTGTGT TTTAGAAAAT GACTTGGATG GCAGTAGGGA ACACCAGAGG GGACAAGTCT GTCAGTTGGA CAGTCCTCAG TTATAATAGA GGCCTGTTCT AAGGCAATGG AGCTCGGAAA AGTGAGGAGA ACACATTACA TTGAGGTGGC ACAGTCTGGT ACTAGTCACT GGACCCACAG CTGTCGAAGA TATCGTGTCC ACCCAACGTA CCCTTTCACG ACAACGAATG GGACGGCGTT TCCTGGTCCT TTGGCGTCGT CCTCAAGTTA T TT GAATC GTGTCCTCCC GGCTTTGGCC AACTTACTAT TCTAGGACTT GATTCCTTCA TTCAGTCACA ATTTATTGAG CACCGACTTT GCATCAACCT CTTGCTGAAG ATAACAGTGC TG CAATATA CAGCCCTGCC CTCAGAGCTT ATATAGTAGA GGAGAAAAAG TGAACCCATA ATATACAGTC AGTAGCGAGT ATTTACTAAG TACTTTCTAT TTGCGAGGCC CTGATAAAAG TACTGTCCTG GCCAGGCGCG GTGGCTCACG CCTGTAATTC CAGCACTTTG GGAGGTCGAG GTGGGCAGAT CACCTAAGGT CAGGAGTTCG AGATCAGCCT GGCTAACATG GGGAAACCCC GTCTCTACTA AAAATGGAAA AATTAGCTGG GCATGGTGGC GGGCGCCTGT AATCCCAGCT ACTCGGGAGG CTGAGACAGG AGAATGACTT GAACCCAGGA GTTGCAGTGG CCAAGATAAG ATAGCGCCAT TGTACTCCAG CCTGGGTAAC ACAGCGAGAC TGTGTCTCAA AAAAAAAAAA AA■3' (SEQ. ID NO: 21)

The deduced protein sequence for the above 373 bp nucleic acid sequence is shown in Table 11 below. Table 11: Amino Acid Sequence Corresponding to the Extended Nucleic Acid Sequence

GLXKYGQVPYCKGYPVRCVENTGFIL ETVKPLNRRVTXVTLSNLCFRKXLG QXGTPEGTSL SVGQSSVIIEACSKAMELGKVRRTHYIEVAQSGTSH THSCRRYRVHPTYPFTTTNGTAFP# (SEQ. ID NO:22)

#, X denotes uncertain amino acid

The deduced amino acid sequence for the extended 569 bp MAG protein is as shown in Table 12 below. Table 12: Extended Amino Acid Sequence Corresponding to 569 Nucleic Acid Sequence

VL RRPQVILESCPPSFGQLTILGLDSFIQSQFIEHRLCIKL LKITLMMPSPPGFGQLTILGI^DSFIQSQFI EHRLCIKLLLKITVLTIYSPALRAYIVEEKK** (SEQ. ID NO:23) X denotes uncertain amino acid

The extended partial sequence of the MAG gene disclosed in this patent consists of 373 base pairs (bp). This DNA sequence was tested for homology with the Advanced BLAST software and found not to have any similarity with other existing genes in the GenBank data base. The present extension elongates the DNA sequence at the 5' end of the gene. The present method relied on the screening of a λ library obtained from Hep G2 human hepatoma cell culture.

Although the invention has been described with reference to presently preferred embodiments, it should be understood that various modifications can be made without departing from the spirit of the invention.

Claims

1. A polypeptide, comprising an oligopeptide selected from the group consisting of SEQ. ID NO: 2, SEQ. ID NO: 8, SEQ. ID NO: 9, seq. id no:23 antibody binding fragments thereof about 7 to 80 amino acids long, pharmaceutically acceptable salts thereof and mixtures thereof.

2. The polypeptide of claim 1, comprising an oligopeptide selected from the group consisting of SEQ. ID NO: 9, antibody binding fragments thereof about 7 to 80 amino acids long, pharmaceutically acceptable salts thereof and mixtures thereof.

3. The polypeptide of claim 1, comprising an oligopeptide selected from the group consisting of SEQ. ID NO: 2, antibody binding fragments thereof about 7 to 80 amino acids long, pharmaceutically acceptable salts thereof and mixtures thereof.

4. The polypeptide of claim 1 , comprising an oligopeptide The polypeptide of claim 1, comprising an oligopeptide selected from the group consisting of SEQ. ID NO: 8, antibody binding fragments thereof about 7 to 80 amino acids long, pharmaceutically acceptable salts thereof and mixtures thereof.

5. The polypeptide of claim 1 , comprising an oligopeptide consisting of antibody binding fragments of SEQ. ID NO: 2 about 10 to 60 amino acids long, pharmaceutically acceptable salts thereof and mixtures thereof.

6. The polypeptide of claim 1, comprising an oligopeptide consisting of antibody binding fragments of SEQ. ID NO: 8 about 10 to 60 amino acids long, pharmaceutically acceptable salts thereof and mixtures thereof.

7. The polypeptide of claim 1, comprising an oligopeptide consisting of antibody binding fragments of SEQ. ID NO: 9 about 10 to 60 amino acids long, pharmaceutically acceptable salts thereof and mixtures thereof.

8. A composition, comprising the polypeptide of claim 1, and a carrier.

9. The composition of claim 8, wherein the carrier comprises a biologically acceptable carrier.

10. The composition of claim 9, wherein the carrier comprises a pharmaceutically acceptable carrier.

11. A liver disease diagnostic kit, comprising the polypeptide of claim 1 ; and instructions for its use in the detection of antibody or antibody fragments in biological samples.

12. A polynucleotide, comprising an oligonucleotide selected from the group consisting of oligonucleotides encoding the polypeptide of claim 1.

13. The polynucleotide of claim 12, comprising an oligonucleotide consisting of SEQ. ID NO: 2 and pharmaceutically acceptable salts thereof.

14. The polynucleotide of claim 12, comprising an oligonucleotide consisting of SEQ. ID NO:

8 and salts thereof.

15. The polynucleotide of claim 12, comprising an oligonucleotide consisting of SEQ. ID NO:

9 and salts thereof.

16. The polynucleotide of claim 12, comprising an oligopeptide selected from the group consisting of oligonucleotides encoding antibody binding fragments of SEQ. ID No: 2, oligonucleotides complementary thereto and salts thereof.

17. The polynucleotide of claim 12, comprising an oligopeptide selected from the group consisting of oligonucleotides encoding antibody binding fragments of SEQ. ID NO: 8, oligonucleotides complementary thereto and salts thereof.

18. The polynucleotide of claim 12, comprising an oligopeptide selected from the group consisting of oligonucleotides encoding antibody binding fragments of SEQ. ID NO: 9, oligonucleotides complementary thereto and salts thereof.

19. The polynucleotide of claim 12, comprising an oligonucleotide selected from the group consisting of nucleotidse 24-132 of SEQ. ID NOJ, nucleotide 24-134 of SEQ. ID NO: 7, oligonucleotides complementary thereto, probes consisting of fragments about 12 to 180 nucleotides long, primers thereof consisting of complementary fragments thereof and salts thereof.

20. The polynucleotide of claim 19, comprising an oligonucleotide selected from the group consisting of nucleotides 24-132 of SEQ. ID NOJ , oligonucleotides complementary thereto, probes consisting of fragments about 7 to 50 nucleotides long, primers thereof consisting of complementary fragments thereof and salts thereof.

21. The polynucleotide of claim 19, comprising an oligonucleotide selected from the group consisting of nucleotides 24-134 of SEQ. ID NO: 7, oligonucleotides complementary thereto, probes consisting of fragments about 7 to 50 nucleotides long, primers thereof consisting of complementary fragments thereof and salts thereof.

22. The polynucleotide of claim 19, comprising an oligonucleotide selected from the group consisting of nucleotides 24-134 of SEQ. ID NO: 7 and salts thereof.

23. The polynucleotide of claim 20, comprising an oligonucleotide selected from the group consisting of nucleotides 24-132 of SEQ. ID NOJ , probes consisting of fragments thereof about 7 to 50 nucleotide long and salts thereof.

24. The polynucleotide of claim 20, comprising an oligonucleotide selected from the group consisting of oligonucleotides complementary to nucleotides 24-132 of SEQ. ID NOJ, primers consisting of fragments thereof about 7 to 50 nucleotides long and salts thereof.

25. The polynucleotide of claim 21, comprising an oligonucleotide selected from the group consisting of nucleotides 24-134 of SEQ. ID NO: 7, probes consisting of fragments thereof about 7 to 50 nucleotides long and salts thereof.

26. The polynucleotide of claim 21 , comprising an oligonucleotide selected from the group consisting of oligonucleotides complementary to nucleotides 24-134 of SEQ. ID NO: 7, and salts thereof.

27. The polynucleotide of claim 21, comprising an oligonucleotide selected from the group consisting of probes consisting of fragments of nucleotides 24-134 of SEQ. ID NO: 7 about 7 to 50 nucleotides long and salts thereof.

28. The polynucleotide of claim 21, comprising an oligonucleotide selected from the group consisting of those consisting of oligonucleotides complementaiy to SEQ. ID NO: 7, primers consisting of fragments thereof about 7 to 50 nucleotides long and salts thereof.

29. A probe, comprising an oligonucleotide consisting essentially of at least a number of nucleotide effective to hybridize under stringent conditions to the polynucleic acid of claim 12.

30. The probe of claim 29, wherein the oligonucleotide consists essentially of at least 40 contiguous nucleic acid residues of polynucleic acids encoding SEQ. ID No: 2, SEQ. ID NO: 8, SEQ. ID NO: 9, fragments thereof or polynucleic acids complementary thereto.

31. The probe of claim 30, wherein the oligonucleotide consists essentially of at least 60 contiguous nucleic acid residues.

32. The probe of claim 31, wherein the oligonucleotide consists essentially of at least 150 contiguous nucleic acid residues.

33. The probe of claim 29, which is labeled.

34. The probe of claim 33, wherein the label is selected from radiolabels and fluorescent labels.

35. The probe of claim 34, being a radiolabeled probe selected from the group consisting of ³²P, ¹⁴C, ^l251, ³H, and ³⁵S labeled probes.

36. The probe of claim 34, being a fluorescently labeled probe.

37. The probe of claim 34, wherein the label comprises a protein.

38. The probe of claim 37, selected from the group consisting of biotin and biotin analogue labeled probes.

39. The probe of claim 37, wherein the protein is radiolabeled or fluorescently labeled.

40. The probe of claim 37, wherein the protein comprises a single-stranded histone binding protein.

41. The probe of claim 29, wherein the oligonucleotide consists essentially of at least a number of nucleotide effective to hybridize under stringent conditions to polynucleic acids encoding SEQ. ID No: 2.

42. The probe of claim 41 , wherein the oligonucleotide consists essentially of at least a number of nucleotide effective to hybridize under stringent conditions to nucleotide 24-132 of SEQ. ID No: 1.

43. The probe of claim 29, wherein the oligonucleotide consists essentially of at least a number of nucleotide effective to hybridize under stringent conditions to polynucleic acids complementary to those encoding SEQ. ID No: 2.

44. The probe of claim 43, wherein the oligonucleotide consists essentially of at least a number of nucleotide effective to hybridize under stringent conditions to a polynucleotide complementary to nucleotide 24-132 of SEQ. ID No: 1.

45. The probe of claim 29, wherein the oligonucleotide consists essentially of at least a number of nucleotide effective to hybridize under stringent conditions to polynucleic acids encoding SEQ. ID No: 8.

46. The probe of claim 45, wherein the oligonucleotide consists essentially of at least a number of nucleotide effective to hybridize under stringent conditions to nucleotides 24-134 of SEQ. ID No: 7.

47. The probe of claim 29, wherein the oligonucleotide consists essentially of at least a number of nucleotide effective to hybridize under stringent conditions to polynucleic acids encoding SEQ. ID No: 9.

48. The probe of claim 47, wherein the oligonucleotide consists essentially of at least a number of nucleotide effective to hybridize under stringent conditions to nucleotides 24-134 of SEQ. ID No: 7.

49. The probe of claim 29, wherein the oligonucleotide consists essentially of at least a number of nucleotide effective to hybridize under stringent conditions to polynucleic acids complementary to those encoding SEQ. ID No: 8.

50. The probe of claim 49, wherein the oligonucleotide consists essentially of at least a number of nucleotide effective to hybridize under stringent conditions to a polynucleic acid complementary to nucleotides 24-134 of SEQ. ID No: 7.

51. The probe of claim 29, wherein the oligonucleotide consists essentially of at least a number of nucleotide effective to hybridize under stringent conditions to polynucleic acids complementary to those encoding SEQ. ID No: 9.

52. The probe of claim 51, wherein the oligonucleotide consists essentially of at least a number of nucleotide effective to hybridize under stringent conditions to a polynucleic acid complementary to nucleotide 24-134 of SEQ. ID No: 7.

53. A composition comprising the polynucleotide of claim 12; and a carrier.

54. The composition of claim 53, wherein the carrier comprises a biologically acceptable carrier.

55. A method of detecting the presence of a polynucleic acid associated with neoplastic disease, comprising contacting polynucleic acid present in a biological sample with the probe of claim 29, under conditions effective to hybridize polynucleic acid encoding a protein associated with a neoplastic disease, or fragments thereof; allowing the formation of double stranded hybrids between the probe and any hybridizing polynucleic acid, or fragments thereof present in the sample; and detecting the presence of the resulting double stranded hybrids.

56. The method of claim 55, wherein the probe is detectably labeled.

57. The method of claim 55, wherein the polynucleic acid is DNA.

58. The method of claim 55, wherein the polynucleic acid is RNA.

59 The method of claim 55, wherein the neoplastic disease is A LIVER DISEASE selected from the group consisting of liver cirrhosis and hepatocellular carcinoma.

60. The method of claim 55, wherein the hybridization is conducted under stringent conditions.

61. The method of claim 55, wherein the polynucleic acid is separated from other cell components present in the sample by lysis.

62. The method of claim 55, wherein the sample is a tissue sample.

63. A method of diagnosing a neoplastic disease, comprising contacting polynucleic acid present in a biological sample with the probe of claim 29, under conditions effective to hybridize polynucleic acid encoding a protein associated with a neoplastic disease, or fragments thereof; allowing the formation of double stranded hybrids between the probe and any hybridizing polynucleic acid, or fragments thereof present in the sample; and detecting the presence of the resulting double stranded hybrids.

64. The method of claim 63, wherein the probe is detectably labeled.

65. The method of claim 63, wherein the polynucleic acid is DNA.

66. The method of claim 63, wherein the polynucleic acid is RNA.

67. The method of claim 63, wherein the neoplastic disease is a liver disease is selected from the group consisting of liver cirrhosis and hepatocellular carcinoma.

68. The method of claim 63, wherein the hybridization is conducted under stringent conditions

69. The method of claim 63, wherein the polynucleic acid is separated from other cell components present in the sample by lysis.

70. The method of claim 63, wherein the sample is a tissue sample.

71. A construct, comprising the polynucleotide of claim 12; an origin of replication; and a promoter.

72. A vector, carrying the polynucleotide of claim 12.

73. The vector of claim 72, being an expression vector.

74. A composition, comprising the vector of claim 72, and a carrier

75. A host cell, transfected with the polynucleotide of claim 12.

76. A host cell, transfected with the constract of claim 71.

77. A host cell, transfected with the vector of claim 72.

78. A method of amplifying the polynucleotide, compnsing culturmg a host cell transfected with the polynucleotide of claim 12, in a growth medium, and under amplifying conditions; and allowing the polynucleotide to accumulate.

79. The method of claim 78, further comprising separating the polynucleotide from the medium, and the cells.

80. A method of producing an polypeptide associated with neoplastic liver disease, comprising cultoring the host cell of claim 75, where the vector comprises an expression vector, in an expression medium and under conditions effective to express the oligopeptide encoded by the probe; and allowing the polypeptide to accumulate.

81. The method of claim 80, further comprising separating the polypeptide from the medium, and the cells.

82. The method of claim 80, wherein the sample is a tissue sample.

83. A neoplastic liver disease diagnostic kit, comprising the polypeptide of claim 12; and instnictions for its use.

84. mRNA, coiresponding to the polypeptide of claim 12.

85. Antibody selectively binding the polypeptide of claim 1.

86. The antibody of claim 85, which is a polyclonal antibody.

87. The antibody of claim 85, which is a monoclonal antibody.

88. A method of detecting the presence of a polypeptide associated with neoplastic disease, comprising obtaining a biological sample suspected of comprising the polypeptide; contacting the sample with the antibody of claim 85, under conditions effective to allow binding of any polypeptide with the antibody and the formation of polypeptide-antibody complexes; and detecting the formation of any polypeptide-antibody complexes.

89. A method of detecting the presence of antibody associated with neoplastic disease, comprising obtaining a biological sample suspected of comprising the antibody; contacting the sample with the polypeptide of claim 1 , under conditions effective to allow binding of the polypeptide with any antibody and the formation of polypeptide-antibody complexes; and detecting the formation of any polypeptide-antibody complexes.