WO1992016656A1 - Gene mutated in colorectal cancer of humans - Google Patents

Gene mutated in colorectal cancer of humans Download PDF

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Publication number
WO1992016656A1
WO1992016656A1 PCT/US1992/000377 US9200377W WO9216656A1 WO 1992016656 A1 WO1992016656 A1 WO 1992016656A1 US 9200377 W US9200377 W US 9200377W WO 9216656 A1 WO9216656 A1 WO 9216656A1
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Prior art keywords
mcc
wild
type
gene
alteration
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PCT/US1992/000377
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French (fr)
Inventor
Bert Vogelstein
Kenneth W. Kinzler
Raymond L. White
Yusuke Nakamura
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CANCER INSTITUTE JAPANESE FOUNDATION FOR CANCER
Japanese Foundation for Cancer Research
Johns Hopkins University
University of Utah
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CANCER INSTITUTE JAPANESE FOUNDATION FOR CANCER
Japanese Foundation for Cancer Research
Johns Hopkins University
University of Utah
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Priority to DE69231245T priority Critical patent/DE69231245T2/en
Priority to AU13302/92A priority patent/AU664834B2/en
Priority to JP50475792A priority patent/JP3501802B2/en
Priority to AT92905276T priority patent/ATE194660T1/en
Priority to DK92905276T priority patent/DK0580596T3/en
Priority to EP92905276A priority patent/EP0580596B1/en
Publication of WO1992016656A1 publication Critical patent/WO1992016656A1/en
Anticipated expiration legal-status Critical
Priority to GR20000402138T priority patent/GR3034446T3/en
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/30—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells
    • C07K16/3046—Stomach, Intestines
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/118—Prognosis of disease development

Definitions

  • the invention relates to the area of cancer diagnostics and therapeutics. More particularly, the invention relates to detection of the alteration of wild-type MCC genes in tumor tissues. In addition, it relates to therapeutic intervention to restore the function of MCC gene product. BACKGROUND OF THE INVENTION
  • this chromosome region harbors the gene responsible for familial adenoma tous polyposis (FAP), an autosomal-dominant, inherited disease in which affected individuals develop hundreds to thousands of adeno atous polyps, some of which progress to malignancy. Additionally, this chromosomal region is often deleted from the adenomas (Vogelstein et al., N. Engl. J. Med., vol. 319, pg. 525 (1988)) and carcinomas (Vogelstein et al., N. Engl. J. Med., vol. 319, pg. 525 (1988); Solomon et al., Nature, vol. 328, pg.
  • FAP familial adenoma tous polyposis
  • a method of diagnosing or prognosing a neoplastic tissue of a human comprising: isolating a tissue from a human; and detecting alteration of wild-type MCC genes or their expression products from said tissue, said alteration indicating neoplasia of the tissue.
  • a method for supplying wild-type MCC gene function to a cell which has lost said gene function by virtue of a mutation in the MCC gene comprising: introducing a wild-type MCC gene into a cell which has lost said gene function such that said wild-type gene is expressed in the cell.
  • a method of supplying wild-type MCC gene function to a cell comprising introducing a portion of a wild-type MCC gene into a cell which has lost said gene function such that said portion is expressed in the cell, said portion encoding a part of the MCC protein which is required for non-neoplastic growth of said cell.
  • Synthetic peptides or drugs can also be used to mimic MCC function in cells which have altered MCC expression.
  • a pair of single stranded primers is provided for determination of the nudeotide sequence of the MCC gene by polymerase chain reaction.
  • the sequence of said pair of sin ⁇ gle stranded DNA primers is derived from chromosome 5q band 21, said pair of primers allowing synthesis of MCC gene coding sequences.
  • a nucleic acid probe is provided which is complementary to human wild- type MCC gene coding sequences and which can form mismatches with mutant MCC genes, thereby allowing their detection by enzymatic or chemi ⁇ cal cleavage or by shifts in electrophoretic mobility.
  • a method for detecting the presence of a neoplastic tissue in a human.
  • the method comprises isolating a body sample from a human; detecting in said sample alteration of a wild-type MCC gene sequence or wild-type MCC expression product, said alteration indicating the presence of a neoplastic tissue in the human.
  • a method of detecting genetic predisposition to cancer in a human, comprising: isolating a human sample selected from the group consisting of blood and fetal tissue; detecting alteration of wild-type MCC gene coding sequences or their expression products from the sample, said alteration indicat ⁇ ing genetic predisposition to cancer.
  • a cDNA molecule which comprises the coding sequence of the MCC gene.
  • a preparation of the human MCC protein is provided which is substantially free of other human pro ⁇ teins.
  • the amino acid sequence of the protein is shown in SEQ ID NO: 2.
  • the present invention provides the art with the information that the MCC gene, a heretofore unknown gene is, in fact, a target of mutational alterations on chromosome 5q21 and that these alterations are associated with the process of tumorigenesis. This information allows highly specific assays to be performed to assess the neoplastic status of a particular tissue or the predisposition to cancer of an individual. BRIEF DESCRIPTION OF THE DRAWINGS
  • Figure 1 shows a Southern blot analysis of tumor T14 demon ⁇ strating a somatic ehange.
  • Lanes 1 an 2 contain 5 ⁇ g of DNA iso ⁇ lated from normal tissue of patient T14;
  • Lanes 3 and 4 contain 5 ug of DNA isolated from the T14 colon carcinoma.
  • Lanes 1 and 3 were cleaved with Eco RI;
  • Lanes 2 and 4 were cleaved with Pst I.
  • the Southern blot in panel A was hybridized to a subclone of cosmid 5.71 (5.71-3).
  • Panels B (3 hour exposure) and C (20 hour exposure) show the same Southern blot hybridized with the abnormal 11 kb fragment cloned from the T14 tumor.
  • the daggers indicate the novel alter ⁇ ations in T14.
  • the size markers indicated on the right represent Hind ⁇ i-cleaved lambda phage DNA and HaeLU-cleaved PhiX phage DNA.
  • Figure 2 shows the sequence of putative exons from the 5.71 cosmid.
  • Panel A shows the sequence of the 5.71-5 exon and the related rat exon.
  • Panel B shows the sequence of the 5.71-3 exon and the related rat exon. Rat sequences are listed only where they differ from the human sequence. Lower ease letters signify introns sur ⁇ rounding the exons.
  • the primers used for PCR are demarcated by arrows. Primers P2 and P4 were reversed and complemented relative to the sequence shown.
  • Figure 3 shows the nudeotide sequence of the MCC cDNA and predicted amino acid sequence. The sequence shown represents the composite sequence of seven overlapping clones.
  • Figure 4 shows PCR - RNase Protection Analysis. The analysis was performed on PCR products and the resulting cleavage products separated by denaturing gel electrophoresis.
  • Panel A shows the results of analysis of the exon encoding nudeotides 2305 to 2405. Lanes 1, 2, and 3 show the results obtained from DNA isolated from three different tumors that did not show any changes. Lanes marked T and N show the results obtained from DNA isolated from patient 9l's tumor or normal cells, respectively.
  • Panel B show the results of analysis of the exon encoding nudeotides 1679-1862. Lanes marked T and N show the results obtained from DNA isolated from patient 35's tumor and normal cells, respectively.
  • Figure 5 shows a comparison of MCC and the G Protein acti ⁇ vating region of human m3 muscarinic acetylcholine receptor (mAChR). Connecting lines indicate identities; dots indicate related amino acid residues. Domain A refers to the 10 amino acid region which, when deleted, alters G protein responses. Domain B refers to the 9 amino acids which can mediate specificity of mAChR G protein coupling. DETAILED DESCRIPTION
  • SUBSTITUTE SHEET "Alteration of a wild-type gene" according to the present invention encompasses all forms of mutations — including deletions.
  • the alter ⁇ ation may be due to either rearrangements such as insertions, inver ⁇ sions, and deletions, or to point mutations. Deletions may by of the entire gene or only a portion of the gene. If only a single allele is mutated, an early neoplastic state is indicated. However, if both alleles are mutated then a late neoplastic state is indicated. The find ⁇ ing of MCC mutations thus provides both diagnostic and prognostic information.
  • An MCC allele which is not deleted can be screened for other mutations, such as insertions, small deletions, and point mutations. It is believed that many mutations found in tumor tissues will be those leading to decreased expression of the MCC gene product. However, mutations leading to non-functional gene products would also lead to a cancerous state. Point mutational events may occur in regulatory regions, such as in the promoter of the gene, leading to loss or diminution of expression of the mRNA. Point mutations may also abolish proper RNA processing, leading to loss of expression of the MCC gene product.
  • tissue In order to detect the alteration of the wild-type MCC gene in a tissue, it is helpful to isolate the tissue free from surrounding nor ⁇ mal tissues.
  • Means for enriching a tissue preparation for tumor cells are known in the art.
  • the tissue may be isolated from paraffin or cryostat sections. Cancer cells may also be separated from normal cells by flow cytometry. These as well as other tech ⁇ niques for separating tumor from normal cells are well known in the art. If the tumor tissue is highly contaminated with normal cells, detection of mutations is more difficult.
  • Detection of point mutations may be accomplished by molecu ⁇ lar cloning of the allele (or alleles) present in the tumor tissue and sequencing that allelefe) using techniques well known in the art.
  • the polymerase chain reaction PCR
  • PCR polymerase chain reaction
  • the polymerase chain reaction itself is well known in the art. See, e.g., Saiki et al., Science, Vol. 239, p. 487, 1988; U.S. 4,683,203; and U.S. 4,683,195.
  • Specific primers which can be used in order to amplify the gene will be discussed in more detail below.
  • the ligase chain reaction which is known in the art, can also be used to amplify MCC sequences. See Wu et al., Genomics, vol. 4, pp. 560-569 (1989).
  • a technique known as allele specific PCR can be used. (See Ruano and Kidd, Nucleic Acids Research, vol 17, p. 8392, 1989.) According to this technique, primers are used which hybridize at their 3' ends to a particular MCC mutation. If the particular MCC mutation is not present, an amplification product is not observed. Insertions and deletions of genes can also be detected by cloning, sequencing and amplification.
  • restriction fragment length polymorphism (RFLP) probes for the gene or sur ⁇ rounding marker genes can be used to score alteration of an allele or an insertion in a polymorphic fragment.
  • RFLP restriction fragment length polymorphism
  • Other techniques for detect ⁇ ing insertions and deletions as are known in the art can be used.
  • Alteration of wild-type genes can also be detected on the basis of the alteration of a wild-type expression product of the gene.
  • Such expression products include both the mRNA as well as the protein product itself.
  • the sequences of these products are shown in SEQ ID NOS: 1 and 2.
  • Point mutations may be detected by amplifying and sequencing the mRNA or via molecular cloning of cDNA made from the mRNA.
  • the sequence of the cloned cDNA can be determined . using DNA sequencing techniques which are well known in the art.
  • the cDNA can also be sequenced via the polymerase chain reaction (PCR) which will be discussed in more detail below.
  • PCR polymerase chain reaction
  • Mismatches are hybridized nucleic acid duplexes which are not 100% homologous.
  • the lack of total homology may be due to deletions, insertions, inversions, substi ⁇ tutions or frameshif t mutations.
  • Mismatch detection can be used to detect point mutations in the gene or its mRNA product. While these techniques are less sensitive than sequencing, they are simpler to perform on a large number of tumor samples.
  • An example of a mis ⁇ match cleavage technique is the RNase protection method, which is described in detail in Winter et al., Proc. Natl. Acad. Sci. USA, Vol. 82, p. 7575, 1985 and Meyers et al., Science, Vol. 230, p. 1242, 1985.
  • the method involves the use of a labeled riboprobe which is complementary to the human wild- type gene coding sequence.
  • the riboprobe and either mRNA or DNA isolated from the tumor tissue are annealed (hybridized) together and subsequently digested with the enzyme RNase A which is able to detect some mismatches in a duplex RNA structure. If a mismatch is detected by RNase A, it cleaves at the site of the mismatch.
  • RNA product when the annealed RNA preparation is separated on ' an electrophoretic gel matrix, if a mismatch has been detected and cleaved by RNase A, an RNA product will be seen which is smaller than the full-length duplex RNA for the riboprobe and the mRNA or DNA.
  • the riboprobe need not be the full length of the MCC mRNA or gene but can be a segment of either. If the riboprobe comprises only a segment of the MCC mRNA or gene it will be desirable to use a number of these probes to screen the whole mRNA sequence for mismatches.
  • DNA probes can be used to detect mis ⁇ matches, through enzymatic or chemical cleavage. See, e.g., Cotton et al., Proc. Natl. Acad. Sci. USA, vol. 85, 4397, 1988; and Shenk et al., Proc. Natl. Acad. Sci. USA, vol. 72, p. 989, 1975.
  • mismatches can be detected by shifts in the electrophoretic mobility of mismatched duplexes relative to matched duplexes. See, e.g., Cariello, Human Genetics, vol. 42, p. 726, 1988.
  • the cellular mRNA or DNA which might contain a mutation can be amplified using PCR (see below) before hybridization. Changes in DNA of the MCC gene can also be detected using Southern hybridization, especially if the changes are gross rear ⁇ rangements, such as deletions and insertions.
  • DNA sequences of the MCC gene from the tumor tissue which have been amplified by use of polymerase chain reaction may also be screened using allele-specific probes.
  • These probes are nucleic acid oligomers, each of which contains a region of the MCC gene sequence harboring a known mutation. For example, one oligomer may be about 30 nudeotides in length, corresponding to a portion of the MCC gene sequence.
  • PCR amplification products can be screened to identify the presence of a previously identified mutation in the MCC gene.
  • Hybridization of allele-specific probes with amplified MCC sequences can be per ⁇ formed, for example, on a nylon filter. Hybridization to a particular probe under stringent hybridization conditions indicates the presence of the same mutation in the tumor tissue as in the allele-specific probe.
  • Alteration of MCC mRNA expression can be detected by any technique known in the art. These include Northern blot analysis, PCR amplification and RNase protection. Diminished mRNA expres ⁇ sion indicates an alteration of the wild-type MCC gene.
  • Alteration of wild-type MCC genes can also be detected by screening for alteration of wild-type MCC protein.
  • monoclonal antibodies immunoreactive with MCC can be used to screen a tissue. Lack of cognate antigen would indicate an MCC mutation.
  • Antibodies specific for products of mutant alleles could also be used to detect mutant MCC gene product.
  • immunological assays could be done in any convenient format known in the art. These include Western blots, immunohistochemieal assays and ELISA assays. Any means for detecting an altered MCC protein can be used to detect alteration of wild-type MCC genes. Functional assays can be used, such as protein binding determinations. For example, it is believed that MCC protein binds to a G protein.
  • an assay for the binding partner to that G protein can be employed.
  • assays can be used which detect MCC biochemical function. It is believed that MCC is involved in phospholipid metabolism. Thus, assaying the enzymatic products of the involved phospholipid meta ⁇ bolic pathway can be used to determine MCC activity. Finding a mutant MCC gene product indicates alteration of a wild-type MCC gene.
  • Mutant MCC genes or gene products can also be detected in other human body samples, such as, serum, stool, urine and sputum.
  • the same techniques discussed above for detection of mutant MCC genes or gene products in tissues can be applied to other body sam ⁇ ples. Cancer cells are sloughed off from tumors and appear in such body samples.
  • the MCC gene product itself may be secreted into the extracellular space and found in these body samples even in the absence of cancer cells. By screening such body samples, a simple early diagnosis can be achieved for many types of cancers. In addition, the progress of chemotherapy or radiotherapy can be monitored more easily by testing such body samples for mutant MCC genes or gene products.
  • the methods of diagnosis of the present invention are applica ⁇ ble to any tumor in which MCC has a role in tumorigenesis.
  • Deletions of chromosome arm 5q have been observed in tumors of lung, breast, colon, rectum, bladder, liver, sarcomas, stomach and prostate, as well as inleukemias and lymphomas. Thus these are likely to be tumors in which MCC has a role.
  • the diagnostic method of the present inven ⁇ tion is useful for clinicians so that they can decide upon an appropri ⁇ ate course of treatment. For example, a tumor displaying alteration of both MCC alleles might suggest a more aggressive therapeutic regi ⁇ men than a tumor displaying alteration of only one MCC allele.
  • the primer pairs of the present invention are useful for deter ⁇ mination of the nudeotide sequence of the MCC gene using the polymerase chain reaction.
  • the pairs of single stranded DNA primers can be annealed to sequences within or surrounding the MCC gene on chromosome 5q in order to prime amplifying DNA synthesis of the MCC gene itself.
  • a complete set of these primers allows synthesis of all of the nudeotides of the MCC gene coding sequences, i.e., the exons.
  • the set of primers preferably allows synthesis of both intron . and exon sequences. Allele specific primers can also be used. Such primers anneal only to particular MCC mutant alleles, and thus will only amplify a product in the presence of the mutant allele as a template.
  • primers may have restriction enzyme site sequences appended to their 5' ends.
  • all nudeotides of the primers are derived from MCC sequences or sequences adjacent to MCC except the few nudeotides necessary to form a restriction enzyme site.
  • the primers themselves can be synthesized using techniques which are well known in the art. Generally, the primers can be made using synthesizing machines which are commercially available. Given the sequence of the MCC open reading frame shown in Figure 3, design of particular primers is well within the skill of the art.
  • the nucleic a d probes provided by the present invention are useful for a number of purposes. They can be used in Southern hybrid ⁇ ization to genomic DNA and in the RNase protection method for detecting point mutations already discussed above.
  • the probes can be used to detect PCR amplification products. They may also be used to detect mismatches with the MCC gene or mRNA using other tech ⁇ niques. Mismatches can be detected using either enzymes (e.g., SI nuclease), chemicals (e.g., hydroxylamine or osmium tetroxide and piperidine), or changes in electrophoretic mobility of mismatched hybrids as compared to totally matched hybrids. These techniques are known in the art. See, Cotton, supra, Shenk, supra.
  • the probes are complementary to MCC gene coding sequences, although probes to certain introns are also contem ⁇ plated.
  • An entire battery of nucleic acid probes is used to compose a kit for detecting alteration of wild-type MCC genes. The kit allows for hybridization to the entire MCC gene. The probes may overlap with each other or be contiguous.
  • a riboprobe is used to detect mismatches with mRNA, it is complementary to the mRNA of the human wild-type MCC gene.
  • the riboprobe thus is an anti-sense probe in that it does not code for the MCC protein because it is of the opposite polarity to the sense strand.
  • the riboprobe generally will be labeled with a radioactive, colorimetric, or fluorometric materials, which can be accomplished by any means known in the art. If the riboprobe is used to detect mis ⁇ matches with DNA it can be of either polarity, sense or anti-sense. Similarly, DNA probes also may be used to detect mismatches.
  • Nucleic acid probes may also be complementary to mutant alleles of MCC gene. These are useful to detect similar mutations in other patients on the basis of hybridization rather than mismatches. These are discussed above and referred to as allele-specific probes.
  • the MCC probes can also be used in Southern hybridizations to genomic DNA to detect gross chromosomal changes such as deletions and insertions.
  • the probes can also be used to select cDNA clones of MCC genes from tumor and normal tissues. In addi- ' tion, the probes can be used to detect MCC mRNA in tissues to deter ⁇ mine if expression is diminished as a result of alteration of wild-type MCC genes.
  • SEQ ID NO:l design of particular probes is well within the skill of the ordinary artisan.
  • a method is also provided of supplying wild-type MCC function to a cell which carries mutant MCC alleles. Supplying such function should suppress neoplastic growth of the recipient cells.
  • the wild-type MCC gene or a part of the gene may be introduced into the cell in a vector such that the gene remains extrachromosomal. In such a situation the gene will be expressed by the cell from the extrachromosomal location. If a gene portion is introduced and expressed in a cell carrying a mutant MCC allele, the gene portion should encode a part of the MCC protein which is required for non-neoplastic growth of the cell.
  • More pre ⁇ ferred is the situation where the wild-type MCC gene or a part of it is introduced into the mutant cell in such a way that it recombines with the endogenous mutant MCC gene present in the cell.
  • Such recombi ⁇ nation requires a double recombination event which results in the correction of the MCC gene mutation.
  • Vectors for introduction of genes both for recombination and for extrachromosomal maintenance are known in the art and any suitable vector may be used.
  • Methods for introducing DNA into cells such as electroporation, calcium phos ⁇ phate co-precipitation and viral transduction are known in the art and the ehoice of method is within the competence of the routineer.
  • Cells transformed with the wild-type MCC-gene can be used as model systems to study cancer remission and drug treatments which promote such remission.
  • Polypeptides which have MCC activity can be supplied to cells which carry mutant or missing MCC alleles.
  • the sequence of the MCC protein is disclosed in Figure 3 (SEQ ID NO:2).
  • Protein can be produced by expression of the cDNA sequence in bacteria, for exam ⁇ ple, using known expression vectors.
  • MCC can be extracted from MCC-producing mammalian cells such as brain cells.
  • the techniques of synthetic chemistry can be employed to synthesize MCC protein. Any of such techniques can provide the preparation of the present invention which comprises the MCC gene product having the sequence shown in Figure 3 (SEQ ID NO:2).
  • the preparation is substantially free of other human proteins. This is most readily accomplished by synthesis in a microorganism or in vitro.
  • Active MCC molecules can be introduced into cells by microinjection or by use of liposomes, for example. Alternatively, some such active molecules may be taken up by cells, actively or by diffusion. Extracellular application of MCC gene product may be sufficient to affect tumor growth. Supply of molecules with MCC activity should lead to a partial reversal of the neoplastic state. Other molecules with MCC activity may also be used to effect such a reversal, for example peptides, drugs, or organic compounds.
  • the present invention also provides a preparation of antibodies immunoreactive with a human MCC protein.
  • the antibodies may be polyclonal or monoclonal and may be raised against native MCC pro ⁇ tein, MCC fusion proteins, or mutant MCC proteins.
  • the antibodies should be immunoreactive with MCC epitopes, preferably epitopes not present on other human proteins.
  • the antibodies will immunoprecipitate MCC proteins from solution as well as react with MCC protein on Western or immunoblots of polyacrylamide gels.
  • the anti ⁇ bodies will detect MCC proteins in parrafin or frozen tissue sections, using immunocytochemical techniques. Techniques for raising and purifying antibodies are well known in the art and any such tech ⁇ niques may be chosen to achieve the preparation of the invention.
  • Predisposition to cancers can be ascertained by testing normal tissues of humans for mutations of MCC gene. For example, a person who has inherited a germline MCC mutation would be prone to develop cancers. This can be determined by testing DNA from any tissue of the person's body. Most simply, blood can be drawn and DNA extracted from the cells of the blood. In addition, prenatal diagnosis can be accomplished by testing fetal cells or amniotic fluid for muta ⁇ tions of the MCC gene. Alteration of a wild-type MCC allele, whether for example, by point mutation or by deletion, can be detected by any of the means discussed above. Molecules of cDNA according to the present invention are intron-free, MCC gene coding molecules.
  • the cDNA can also be made using the techniques of synthetic chemis ⁇ try given the sequence disclosed herein.
  • G proteins are known to regulate phospholipase A 2 activity, which generates arachidonic acid from phosphplipids (Role et al., Proc. Natl. Acad. Sci. USA, vol. 84, pg. 3623 (1987); Kurachi et al., Nature, vol. 337, pg. 555 (1989)). Therefore we propose that wild-type MCC protein functions by interacting with a G protein and is involved in phospholipid metabolism.
  • This example demonstrates the detection of a somatic cell gene rearrangement occurring in chromosome 5q21 in a colorectal carcinoma.
  • the new EcoRI fragment was cloned- , and used to probe Southern blots with DNA from tumor T14.
  • the 11 kb clone hybridized to the abnormal 11 kb EcoRI fragment and to the normal 20 kb EcoRI fragment in the tumor as expected ( Figure 1, Panel B).
  • the 11 kb clone detected new fragments in tumor T14 DNA upon digestion with other restriction endonucleases (including Pstl [ Figure 1, Panel C ] ; Hind IE and EcoRV).
  • This example demonstrates the identification of an expressed human gene near the cosmid 5.71 RFLP marker.
  • Primers were derived from the two putative exons. PCR per ⁇ formed with these primers, using cDNA as template, allows detection of putative exons if they are joined by RNA splicing within cells. Contaminating genomic DNA in the RNA preparation does not inter ⁇ fere with this assay, since the intervening intron(s) results in much longer PCR products from genomic DNA than that obtained from the spliced RNA.
  • PCR was performed as described in Baker et al., Cancer Research, vol. 50, pg. 7717 (1990), using 35 cycles of: 95 degrees C for 0.5 minutes, 55 degrees C for 2 minutes, and 70 degrees C for 2 minutes.
  • the PCR product was exactly the size (226 bp) expected if direct splicing of the two putative exons had occurred at the splice sites identified in the human and rat genomic DNA sequences. Cloning and sequencing of the PCR product confirmed that it represented the result of a direct splice between the 5.71-5 and 5.71-3 exons.
  • This example demonstrates the isolation and sequencing of the human MCC cDNA from brain.
  • the PCR product amplified using human cDNA as a template was then labelled and used as a probe to screen a cDNA library from normal human brain. Brain was chosen because the exon-connection assay suggested that MCC was expressed at high levels in this tissue.
  • the cDNA library was constructed from human brain mRNA as described in U. Gubler and B.J. Hoffman, Gene 25, 263 (1983) and the Lambda Zap vector (Stratagene). 1.5 x 10 6 plaques were screened with the PCR product connecting the 5.71-3 and 5.71-5 exons (see Figure 2.)
  • the ORF was surrounded by at least 200 bp of 5' untranslated sequence and 1450 bp of 3' untranslated sequence. There was no evi ⁇ dence of a polyadenylylation tract at the 3' end of any clone.
  • cDNA probes detected RNAs of several seizes (3-10 kb) on Northern blots; we do not know whether these other transcripts represent alterna ⁇ tively spliced forms of the MCC gene or related genes from other loci.
  • sequences of exon boundaries were derived following the screening of human genomic DNA libraries with MCC cDNA probes. Positively hybridizing clones were isolated and small fragments (0.2-3kb) subcloned and sequenced. Primers for amplifying the exons were chosen outside of the splice sites and were as follows: 5'-GAATTCATCAGCACTTCT-3* (SEQ ID NO:3) and
  • 5'-CAGCTCCAAGATGGAGGG-3' (SEQ ID NO:4) for the exon contain ⁇ ing nudeotides 391 to 533, 5'-GGCCCCATGTGCTTTGTT-3' (SEQ ID NO:5) and 5'-AGAGGGACTCTGGAGACA-3* (SEQ ID NO:6) for the exon containing nudeotides 1575 to 1678,
  • RNAse protection assay was performed as described by Winter et al., Proc. Natl. Acad.
  • Hybridizations were carried out in 9 ul of hybridization solution containing 1 ul of the appropriate PCR reac ⁇ tion and 3 P labeled transcript (200,000 dpm) for 2 hours at 50 degrees C.
  • RNase treatment was initiated by addition of 90 ul of RNase solu ⁇ tion (0.2 M NaCl, 0.1 M LiCl, 20 mM Tris-HCl, pH 7.5, ImM EDTA, 25 ug/ml RNase A) and incubated 1 hour at 37 degrees C.
  • RNase treat ⁇ ment was terminated by the addition of proteinase K solution (5 mg/ml proteinase K in 10% SDS) and incubated 1 hour at 37 degrees C. The solution was then extracted one time with PC 9 (3 parts phenol and 4 parts chloroform equilibrated with 2 parts 0.5 M Tris-HCl, pH 9.0, 10 mM EDTA, 10 mM NaCl) and 20 ul of the aqueous phase was collected and combined wtih 20 ul of loading buffer (0.3% W/V xylene cyanol, 0.3% W/V bromophenol blue in formamide). The samples were then heated at 94 degrees C for 4 minutes and loaded directly on a denaturing polyacrylamide gel. Two separate assays were performed for each exon, one with each strand as labeled transcript.
  • the first exon (containing nudeotides 391 to 533) of four tested showed no variants among 100 colorectal tumors tested.
  • Analysis of the exon containing nudeotides 1575 to 1678 identified five tumors with identical variations in their RNase protection pattern. Cloning and sequencing of the variant PCR product from two of the five tumors indicated that it resulted from a C to T transition at nudeotide 1676 which resulted in a coding change from proline to leucine.
  • This variant presumably represents a polymorphism, as it was found in five individuals and was present in DNA from the normal tissue of two of the five patients whose tumors showed the variant (the other three were not tested).
  • CCTCCTGCAG CAATGGCTCG TCCGTGAAAC GCGAGCCACG GCTGCTCTTT TTAAGAGTGC 60
  • GGCCAACAGC AACCTGGTGG CTGCCTATGA GAAAGCAAAG AAAAAGCATC AAAACAAACT 2580
  • ACAGGTGTTA CTTACAGTCC CAGATACACT AAAGTTACAA ACAGACCACC ACCAGGACTG 3360
  • Arg lie Thr Glu Leu His Ser Val lie Ala Glu Leu Asn Lys Lys lie 85 90 95 Asp Arg Leu Gin Gly Thr Thr lie Arg Glu Glu Asp Glu Tyr Ser Glu 100 105 110
  • MOLECULE TYPE DNA (genomic)
  • MOLECULE TYPE DNA (genomic)
  • MOLECULE TYPE DNA (genomic)
  • MOLECULE TYPE DNA (genomic)
  • MOLECULE TYPE DNA (genomic)
  • MOLECULE TYPE DNA (genomic)
  • MOLECULE TYPE DNA (genomic)
  • MOLECULE TYPE DNA (genomic)
  • CAGCACTTCT GTCCTTTTCC CTTATTCCCA G TGC GAG CAG TCC CAC CTC ATG 52
  • MOLECULE TYPE DNA (genomic)
  • ORGANISM Rattus rattus
  • MOLECULE TYPE DNA (genomic)
  • MOLECULE TYPE protein

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Abstract

A new human gene termed MCC is disclosed. Methods and kits are provided for assessing mutations of the MCC gene in human tissues and body samples. Gross rearrangement and point mutations in MCC are observed in human tumor cells. MCC is expressed in most normal tissues. These results suggest that MCC is a tumor suppressor.

Description

GENE MUTATED IN COLORECTA CANCER OF HUMANS
The U.S. Government has a paid-up license in this invention and the right in limited circumstances to require the patent owner to license others on reasonable terms as provided for by the terms of grants awarded by the National Institutes of Health. TECHNICAL AREA OF THE INVENTION
The invention relates to the area of cancer diagnostics and therapeutics. More particularly, the invention relates to detection of the alteration of wild-type MCC genes in tumor tissues. In addition, it relates to therapeutic intervention to restore the function of MCC gene product. BACKGROUND OF THE INVENTION
According to the model of Knudson for tumorigenesis (Cancer Research, vol. 45, p. 1482, 1985), there are tumor suppressor genes in all normal cells which, when they become non-functional due to mutation, cause neoplastic development. Evidence for this model has been found in the cases of retinoblastoma and colorectal tumors. The implicated suppressor genes in those tumors, RB and p53 and DCC, were found to be deleted or altered in many cases of the tumors stud¬ ied. (Hansen and Cavenee, Cancer Research, vol. 47, pp. 5518-5527 (1987); Baker et al., Science, vol. 244, p. 217 (1989); Fearon et al., Science, vol. 247, p. 49 (1990).)
In order to fully understand the pathogenesis of tumors, it will be necessary to identify the other suppressor genes that play a role in the tumorigenesis process. Prominent among these is the one(s) pre¬ sumptively located at 5q21. Cytogenetic (Herrera et al., Am J. Med. Genet., vol. 25, pg. 473 (1986) and linkage (Leppert et al., Science, vol. 238, pg. 1411 (1987); Bodmer et al., Nature, vol. 328, pg. 614 (1987)) studies have shown that this chromosome region harbors the gene responsible for familial adenoma tous polyposis (FAP), an autosomal-dominant, inherited disease in which affected individuals develop hundreds to thousands of adeno atous polyps, some of which progress to malignancy. Additionally, this chromosomal region is often deleted from the adenomas (Vogelstein et al., N. Engl. J. Med., vol. 319, pg. 525 (1988)) and carcinomas (Vogelstein et al., N. Engl. J. Med., vol. 319, pg. 525 (1988); Solomon et al., Nature, vol. 328, pg. 616 (1987); Sasaki et al., Cancer Research, vol. 49, pg. 4402 (1989); Delattre et al., Lancet, vol. 2, pg. 353 (1989); and Ashton-Rickardt et al., Oncogene, vol. 4, pg. 1169 (1989)) of patients without FAP. Thus, a putative suppressor gene on chromosome 5q21 appears to play a role in the early stages of colorectal neoplasia in both sporadic and famil¬ ial tumors. However, no gene has been identified on 5q21 which is a candidate suppressor gene. Thus there is a need in the art for investi¬ gations of this chromosomal region to identify genes and to determine if any of such genes are associated with the process of tumorigenesis. SUMMARY OF THE INVENTION
It is an object of the present invention to provide a method for diagnosing and prognosing a neoplastic tissue of a human.
It is another object of the invention to provide a method of supplying wild-type MCC gene function to a cell which has lost said gene function.
It is yet another object of the invention to provide a kit for determination of the nudeotide sequence of MCC alleles by the polymerase chain reaction.
It is still another object of the invention to provide nucleic acid probes for detection of mutations in the human MCC gene.
It is another object of the invention to provide a method of detecting genetic predisposition to cancer.
It is still another object of the invention to provide a cDNA molecule encoding the MCC gene product.
It is yet another object of the invention to provide a prepara¬ tion of the human MCC protein.
These and other objects of the invention are provided by one or more of the embodiments which are described below. In one embodi¬ ment of the present invention a method of diagnosing or prognosing a neoplastic tissue of a human is provided comprising: isolating a tissue from a human; and detecting alteration of wild-type MCC genes or their expression products from said tissue, said alteration indicating neoplasia of the tissue.
In another embodiment of the present invention a method is provided for supplying wild-type MCC gene function to a cell which has lost said gene function by virtue of a mutation in the MCC gene, comprising: introducing a wild-type MCC gene into a cell which has lost said gene function such that said wild-type gene is expressed in the cell.
In another embodiment a method of supplying wild-type MCC gene function to a cell is provided comprising introducing a portion of a wild-type MCC gene into a cell which has lost said gene function such that said portion is expressed in the cell, said portion encoding a part of the MCC protein which is required for non-neoplastic growth of said cell. Synthetic peptides or drugs can also be used to mimic MCC function in cells which have altered MCC expression.
In yet another embodiment a pair of single stranded primers is provided for determination of the nudeotide sequence of the MCC gene by polymerase chain reaction. The sequence of said pair of sin¬ gle stranded DNA primers is derived from chromosome 5q band 21, said pair of primers allowing synthesis of MCC gene coding sequences.
In still another embodiment of the invention a nucleic acid probe is provided which is complementary to human wild- type MCC gene coding sequences and which can form mismatches with mutant MCC genes, thereby allowing their detection by enzymatic or chemi¬ cal cleavage or by shifts in electrophoretic mobility.
In another embodiment of the invention a method is provided for detecting the presence of a neoplastic tissue in a human. The method comprises isolating a body sample from a human; detecting in said sample alteration of a wild-type MCC gene sequence or wild-type MCC expression product, said alteration indicating the presence of a neoplastic tissue in the human.
In yet another embodiment a method is provided of detecting genetic predisposition to cancer in a human, comprising: isolating a human sample selected from the group consisting of blood and fetal tissue; detecting alteration of wild-type MCC gene coding sequences or their expression products from the sample, said alteration indicat¬ ing genetic predisposition to cancer.
In still another embodiment a cDNA molecule is provided which comprises the coding sequence of the MCC gene.
In even another embodiment a preparation of the human MCC protein is provided which is substantially free of other human pro¬ teins. The amino acid sequence of the protein is shown in SEQ ID NO: 2.
The present invention provides the art with the information that the MCC gene, a heretofore unknown gene is, in fact, a target of mutational alterations on chromosome 5q21 and that these alterations are associated with the process of tumorigenesis. This information allows highly specific assays to be performed to assess the neoplastic status of a particular tissue or the predisposition to cancer of an individual. BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 shows a Southern blot analysis of tumor T14 demon¬ strating a somatic ehange. Lanes 1 an 2 contain 5 ύg of DNA iso¬ lated from normal tissue of patient T14; Lanes 3 and 4 contain 5 ug of DNA isolated from the T14 colon carcinoma. Lanes 1 and 3 were cleaved with Eco RI; Lanes 2 and 4 were cleaved with Pst I. The Southern blot in panel A was hybridized to a subclone of cosmid 5.71 (5.71-3). Panels B (3 hour exposure) and C (20 hour exposure) show the same Southern blot hybridized with the abnormal 11 kb fragment cloned from the T14 tumor. The daggers indicate the novel alter¬ ations in T14. The size markers indicated on the right represent Hindπi-cleaved lambda phage DNA and HaeLU-cleaved PhiX phage DNA.
Figure 2 shows the sequence of putative exons from the 5.71 cosmid. Panel A shows the sequence of the 5.71-5 exon and the related rat exon. Panel B shows the sequence of the 5.71-3 exon and the related rat exon. Rat sequences are listed only where they differ from the human sequence. Lower ease letters signify introns sur¬ rounding the exons. The primers used for PCR are demarcated by arrows. Primers P2 and P4 were reversed and complemented relative to the sequence shown.
Figure 3 shows the nudeotide sequence of the MCC cDNA and predicted amino acid sequence. The sequence shown represents the composite sequence of seven overlapping clones.
Figure 4 shows PCR - RNase Protection Analysis. The analysis was performed on PCR products and the resulting cleavage products separated by denaturing gel electrophoresis. Panel A shows the results of analysis of the exon encoding nudeotides 2305 to 2405. Lanes 1, 2, and 3 show the results obtained from DNA isolated from three different tumors that did not show any changes. Lanes marked T and N show the results obtained from DNA isolated from patient 9l's tumor or normal cells, respectively. Panel B show the results of analysis of the exon encoding nudeotides 1679-1862. Lanes marked T and N show the results obtained from DNA isolated from patient 35's tumor and normal cells, respectively.
Figure 5 shows a comparison of MCC and the G Protein acti¬ vating region of human m3 muscarinic acetylcholine receptor (mAChR). Connecting lines indicate identities; dots indicate related amino acid residues. Domain A refers to the 10 amino acid region which, when deleted, alters G protein responses. Domain B refers to the 9 amino acids which can mediate specificity of mAChR G protein coupling. DETAILED DESCRIPTION
It is a discovery of the present invention that mutational events associated with tumorigenesis occur in a previously unknown gene on chromosome 5q named here the MCC (Mutated in Colorectal Cancer) gene. Although it was previously known that deletion of alleles on chromosome 5q were common in certain types of cancers, it was not known that a target gene of these deletions was the MCC gene. Further it was not known that other types of mutational events in the MCC gene are also associated with cancers. The mutations of the MCC gene can involve gross rearrangements, such as insertions and deletions. Point mutations have also been observed.
According to the diagnostic and prognostic method of the present invention, alteration of the wild-type gene is detected.
SUBSTITUTE SHEET "Alteration of a wild-type gene" according to the present invention encompasses all forms of mutations — including deletions. The alter¬ ation may be due to either rearrangements such as insertions, inver¬ sions, and deletions, or to point mutations. Deletions may by of the entire gene or only a portion of the gene. If only a single allele is mutated, an early neoplastic state is indicated. However, if both alleles are mutated then a late neoplastic state is indicated. The find¬ ing of MCC mutations thus provides both diagnostic and prognostic information. An MCC allele which is not deleted (e.g., that on the sister chromosome to a chromosome carrying an MCC deletion) can be screened for other mutations, such as insertions, small deletions, and point mutations. It is believed that many mutations found in tumor tissues will be those leading to decreased expression of the MCC gene product. However, mutations leading to non-functional gene products would also lead to a cancerous state. Point mutational events may occur in regulatory regions, such as in the promoter of the gene, leading to loss or diminution of expression of the mRNA. Point mutations may also abolish proper RNA processing, leading to loss of expression of the MCC gene product.
In order to detect the alteration of the wild-type MCC gene in a tissue, it is helpful to isolate the tissue free from surrounding nor¬ mal tissues. Means for enriching a tissue preparation for tumor cells are known in the art. For example, the tissue may be isolated from paraffin or cryostat sections. Cancer cells may also be separated from normal cells by flow cytometry. These as well as other tech¬ niques for separating tumor from normal cells are well known in the art. If the tumor tissue is highly contaminated with normal cells, detection of mutations is more difficult.
Detection of point mutations may be accomplished by molecu¬ lar cloning of the allele (or alleles) present in the tumor tissue and sequencing that allelefe) using techniques well known in the art. Alternatively, the polymerase chain reaction (PCR) can be used to amplify gene sequences directly from a genomic DNA preparation from the tumor tissue. The DNA sequence of the amplified sequences can then be determined. The polymerase chain reaction itself is well known in the art. See, e.g., Saiki et al., Science, Vol. 239, p. 487, 1988; U.S. 4,683,203; and U.S. 4,683,195. Specific primers which can be used in order to amplify the gene will be discussed in more detail below. The ligase chain reaction, which is known in the art, can also be used to amplify MCC sequences. See Wu et al., Genomics, vol. 4, pp. 560-569 (1989). In addition, a technique known as allele specific PCR can be used. (See Ruano and Kidd, Nucleic Acids Research, vol 17, p. 8392, 1989.) According to this technique, primers are used which hybridize at their 3' ends to a particular MCC mutation. If the particular MCC mutation is not present, an amplification product is not observed. Insertions and deletions of genes can also be detected by cloning, sequencing and amplification. In addition, restriction fragment length polymorphism (RFLP) probes for the gene or sur¬ rounding marker genes can be used to score alteration of an allele or an insertion in a polymorphic fragment. Other techniques for detect¬ ing insertions and deletions as are known in the art can be used.
Alteration of wild-type genes can also be detected on the basis of the alteration of a wild-type expression product of the gene. Such expression products include both the mRNA as well as the protein product itself. The sequences of these products are shown in SEQ ID NOS: 1 and 2. Point mutations may be detected by amplifying and sequencing the mRNA or via molecular cloning of cDNA made from the mRNA. The sequence of the cloned cDNA can be determined . using DNA sequencing techniques which are well known in the art. The cDNA can also be sequenced via the polymerase chain reaction (PCR) which will be discussed in more detail below.
Mismatches, according to the present invention are hybridized nucleic acid duplexes which are not 100% homologous. The lack of total homology may be due to deletions, insertions, inversions, substi¬ tutions or frameshif t mutations. Mismatch detection can be used to detect point mutations in the gene or its mRNA product. While these techniques are less sensitive than sequencing, they are simpler to perform on a large number of tumor samples. An example of a mis¬ match cleavage technique is the RNase protection method, which is described in detail in Winter et al., Proc. Natl. Acad. Sci. USA, Vol. 82, p. 7575, 1985 and Meyers et al., Science, Vol. 230, p. 1242, 1985. In the practice of the present invention the method involves the use of a labeled riboprobe which is complementary to the human wild- type gene coding sequence. The riboprobe and either mRNA or DNA isolated from the tumor tissue are annealed (hybridized) together and subsequently digested with the enzyme RNase A which is able to detect some mismatches in a duplex RNA structure. If a mismatch is detected by RNase A, it cleaves at the site of the mismatch. Thus, when the annealed RNA preparation is separated on ' an electrophoretic gel matrix, if a mismatch has been detected and cleaved by RNase A, an RNA product will be seen which is smaller than the full-length duplex RNA for the riboprobe and the mRNA or DNA. The riboprobe need not be the full length of the MCC mRNA or gene but can be a segment of either. If the riboprobe comprises only a segment of the MCC mRNA or gene it will be desirable to use a number of these probes to screen the whole mRNA sequence for mismatches.
In similar fashion, DNA probes can be used to detect mis¬ matches, through enzymatic or chemical cleavage. See, e.g., Cotton et al., Proc. Natl. Acad. Sci. USA, vol. 85, 4397, 1988; and Shenk et al., Proc. Natl. Acad. Sci. USA, vol. 72, p. 989, 1975. Alternatively, mismatches can be detected by shifts in the electrophoretic mobility of mismatched duplexes relative to matched duplexes. See, e.g., Cariello, Human Genetics, vol. 42, p. 726, 1988. With either riboprobes or DNA probes, the cellular mRNA or DNA which might contain a mutation can be amplified using PCR (see below) before hybridization. Changes in DNA of the MCC gene can also be detected using Southern hybridization, especially if the changes are gross rear¬ rangements, such as deletions and insertions.
DNA sequences of the MCC gene from the tumor tissue which have been amplified by use of polymerase chain reaction may also be screened using allele-specific probes. These probes are nucleic acid oligomers, each of which contains a region of the MCC gene sequence harboring a known mutation. For example, one oligomer may be about 30 nudeotides in length, corresponding to a portion of the MCC gene sequence. By use of a battery of such allele-specific probes, PCR amplification products can be screened to identify the presence of a previously identified mutation in the MCC gene. Hybridization of allele-specific probes with amplified MCC sequences can be per¬ formed, for example, on a nylon filter. Hybridization to a particular probe under stringent hybridization conditions indicates the presence of the same mutation in the tumor tissue as in the allele-specific probe.
Alteration of MCC mRNA expression can be detected by any technique known in the art. These include Northern blot analysis, PCR amplification and RNase protection. Diminished mRNA expres¬ sion indicates an alteration of the wild-type MCC gene.
Alteration of wild-type MCC genes can also be detected by screening for alteration of wild-type MCC protein. For example, monoclonal antibodies immunoreactive with MCC can be used to screen a tissue. Lack of cognate antigen would indicate an MCC mutation. Antibodies specific for products of mutant alleles could also be used to detect mutant MCC gene product. Such immunological assays could be done in any convenient format known in the art. These include Western blots, immunohistochemieal assays and ELISA assays. Any means for detecting an altered MCC protein can be used to detect alteration of wild-type MCC genes. Functional assays can be used, such as protein binding determinations. For example, it is believed that MCC protein binds to a G protein. Thus, an assay for the binding partner to that G protein can be employed. In addition, assays can be used which detect MCC biochemical function. It is believed that MCC is involved in phospholipid metabolism. Thus, assaying the enzymatic products of the involved phospholipid meta¬ bolic pathway can be used to determine MCC activity. Finding a mutant MCC gene product indicates alteration of a wild-type MCC gene.
Mutant MCC genes or gene products can also be detected in other human body samples, such as, serum, stool, urine and sputum. The same techniques discussed above for detection of mutant MCC genes or gene products in tissues can be applied to other body sam¬ ples. Cancer cells are sloughed off from tumors and appear in such body samples. In addition, the MCC gene product itself may be secreted into the extracellular space and found in these body samples even in the absence of cancer cells. By screening such body samples, a simple early diagnosis can be achieved for many types of cancers. In addition, the progress of chemotherapy or radiotherapy can be monitored more easily by testing such body samples for mutant MCC genes or gene products.
The methods of diagnosis of the present invention are applica¬ ble to any tumor in which MCC has a role in tumorigenesis. Deletions of chromosome arm 5q have been observed in tumors of lung, breast, colon, rectum, bladder, liver, sarcomas, stomach and prostate, as well as inleukemias and lymphomas. Thus these are likely to be tumors in which MCC has a role. The diagnostic method of the present inven¬ tion is useful for clinicians so that they can decide upon an appropri¬ ate course of treatment. For example, a tumor displaying alteration of both MCC alleles might suggest a more aggressive therapeutic regi¬ men than a tumor displaying alteration of only one MCC allele.
The primer pairs of the present invention are useful for deter¬ mination of the nudeotide sequence of the MCC gene using the polymerase chain reaction. The pairs of single stranded DNA primers can be annealed to sequences within or surrounding the MCC gene on chromosome 5q in order to prime amplifying DNA synthesis of the MCC gene itself. A complete set of these primers allows synthesis of all of the nudeotides of the MCC gene coding sequences, i.e., the exons. The set of primers preferably allows synthesis of both intron . and exon sequences. Allele specific primers can also be used. Such primers anneal only to particular MCC mutant alleles, and thus will only amplify a product in the presence of the mutant allele as a template.
In order to facilitate subsequent cloning of amplified sequences, primers may have restriction enzyme site sequences appended to their 5' ends. Thus, all nudeotides of the primers are derived from MCC sequences or sequences adjacent to MCC except the few nudeotides necessary to form a restriction enzyme site. Such enzymes and sites are well known in the art. The primers themselves can be synthesized using techniques which are well known in the art. Generally, the primers can be made using synthesizing machines which are commercially available. Given the sequence of the MCC open reading frame shown in Figure 3, design of particular primers is well within the skill of the art.
The nucleic a d probes provided by the present invention are useful for a number of purposes. They can be used in Southern hybrid¬ ization to genomic DNA and in the RNase protection method for detecting point mutations already discussed above. The probes can be used to detect PCR amplification products. They may also be used to detect mismatches with the MCC gene or mRNA using other tech¬ niques. Mismatches can be detected using either enzymes (e.g., SI nuclease), chemicals (e.g., hydroxylamine or osmium tetroxide and piperidine), or changes in electrophoretic mobility of mismatched hybrids as compared to totally matched hybrids. These techniques are known in the art. See, Cotton, supra, Shenk, supra. Myers, supra.- Winter, supra, and Novack et al., Proc. Natl. Acad. Sci. USA, vol. 83, p. 586, 1986. Generally, the probes are complementary to MCC gene coding sequences, although probes to certain introns are also contem¬ plated. An entire battery of nucleic acid probes is used to compose a kit for detecting alteration of wild-type MCC genes. The kit allows for hybridization to the entire MCC gene. The probes may overlap with each other or be contiguous.
If a riboprobe is used to detect mismatches with mRNA, it is complementary to the mRNA of the human wild-type MCC gene. The riboprobe thus is an anti-sense probe in that it does not code for the MCC protein because it is of the opposite polarity to the sense strand. The riboprobe generally will be labeled with a radioactive, colorimetric, or fluorometric materials, which can be accomplished by any means known in the art. If the riboprobe is used to detect mis¬ matches with DNA it can be of either polarity, sense or anti-sense. Similarly, DNA probes also may be used to detect mismatches.
Nucleic acid probes may also be complementary to mutant alleles of MCC gene. These are useful to detect similar mutations in other patients on the basis of hybridization rather than mismatches. These are discussed above and referred to as allele-specific probes. As mentioned above, the MCC probes can also be used in Southern hybridizations to genomic DNA to detect gross chromosomal changes such as deletions and insertions. The probes can also be used to select cDNA clones of MCC genes from tumor and normal tissues. In addi- ' tion, the probes can be used to detect MCC mRNA in tissues to deter¬ mine if expression is diminished as a result of alteration of wild-type MCC genes. Provided with the MCC coding sequence shown in Figure 3 (SEQ ID NO:l), design of particular probes is well within the skill of the ordinary artisan.
According to the present invention a method is also provided of supplying wild-type MCC function to a cell which carries mutant MCC alleles. Supplying such function should suppress neoplastic growth of the recipient cells. The wild-type MCC gene or a part of the gene may be introduced into the cell in a vector such that the gene remains extrachromosomal. In such a situation the gene will be expressed by the cell from the extrachromosomal location. If a gene portion is introduced and expressed in a cell carrying a mutant MCC allele, the gene portion should encode a part of the MCC protein which is required for non-neoplastic growth of the cell. More pre¬ ferred is the situation where the wild-type MCC gene or a part of it is introduced into the mutant cell in such a way that it recombines with the endogenous mutant MCC gene present in the cell. Such recombi¬ nation requires a double recombination event which results in the correction of the MCC gene mutation. Vectors for introduction of genes both for recombination and for extrachromosomal maintenance are known in the art and any suitable vector may be used. Methods for introducing DNA into cells such as electroporation, calcium phos¬ phate co-precipitation and viral transduction are known in the art and the ehoice of method is within the competence of the routineer. Cells transformed with the wild-type MCC-gene can be used as model systems to study cancer remission and drug treatments which promote such remission.
Polypeptides which have MCC activity can be supplied to cells which carry mutant or missing MCC alleles. The sequence of the MCC protein is disclosed in Figure 3 (SEQ ID NO:2). Protein can be produced by expression of the cDNA sequence in bacteria, for exam¬ ple, using known expression vectors. Alternatively, MCC can be extracted from MCC-producing mammalian cells such as brain cells. In addition, the techniques of synthetic chemistry can be employed to synthesize MCC protein. Any of such techniques can provide the preparation of the present invention which comprises the MCC gene product having the sequence shown in Figure 3 (SEQ ID NO:2). The preparation is substantially free of other human proteins. This is most readily accomplished by synthesis in a microorganism or in vitro. Active MCC molecules can be introduced into cells by microinjection or by use of liposomes, for example. Alternatively, some such active molecules may be taken up by cells, actively or by diffusion. Extracellular application of MCC gene product may be sufficient to affect tumor growth. Supply of molecules with MCC activity should lead to a partial reversal of the neoplastic state. Other molecules with MCC activity may also be used to effect such a reversal, for example peptides, drugs, or organic compounds.
The present invention also provides a preparation of antibodies immunoreactive with a human MCC protein. The antibodies may be polyclonal or monoclonal and may be raised against native MCC pro¬ tein, MCC fusion proteins, or mutant MCC proteins. The antibodies should be immunoreactive with MCC epitopes, preferably epitopes not present on other human proteins. In a preferred embodiment of the invention the antibodies will immunoprecipitate MCC proteins from solution as well as react with MCC protein on Western or immunoblots of polyacrylamide gels. In another preferred embodiment, the anti¬ bodies will detect MCC proteins in parrafin or frozen tissue sections, using immunocytochemical techniques. Techniques for raising and purifying antibodies are well known in the art and any such tech¬ niques may be chosen to achieve the preparation of the invention.
Predisposition to cancers can be ascertained by testing normal tissues of humans for mutations of MCC gene. For example, a person who has inherited a germline MCC mutation would be prone to develop cancers. This can be determined by testing DNA from any tissue of the person's body. Most simply, blood can be drawn and DNA extracted from the cells of the blood. In addition, prenatal diagnosis can be accomplished by testing fetal cells or amniotic fluid for muta¬ tions of the MCC gene. Alteration of a wild-type MCC allele, whether for example, by point mutation or by deletion, can be detected by any of the means discussed above. Molecules of cDNA according to the present invention are intron-free, MCC gene coding molecules. They can be made by reverse transcriptase using the MCC mRNA as a template. These molecules can be propagated in vectors and cell lines as is known in the art. Such molecules have the sequence shown in SEQ ID NO: 1. The cDNA can also be made using the techniques of synthetic chemis¬ try given the sequence disclosed herein.
A short region of homology has been identified between MCC and the human m3 muscarinic acetylcholine receptor (mAChR). This homology was largely confined to 19 residues in which the carboxy-terminal 6 amino acids (KELAGL) were identical (See Figure 5 and SEQ ID NO: 11). Initially, it was not known whether this homology was significant, because many other proteins had higher- levels of global homology (though few had six contiguous amino acids in common). During a search for mutations, however, a study on the sequence elements controlling G protein activation by mAChR subtypes was published (Lechleiter et al., EMBO J., p. 4381 (1990)). It was shown that a 21 amino acid region from the m3 mAChR com¬ pletely mediated G protein specificity when substituted for the 21 amino acids of m2 mAChR at the analogous protein position. These 21 residues overlapped the 19 amino acid homology between MCC and m3 mAChR (Figure 5). A ten residue deletion (Figure 5, domain A), which included the two amino-terminal amino acids of the KELAGL motif, completely altered the kinetics and magnitude of the G protein mediated response. Moreover, a 9-residue subdomain (Figure 5, domain B) which included the 4 carboxy-terminal amino acids of KELAGL, was sufficient for specifying the activation of the m3 G protein pathway when transferred to the m2 mAChR.
This connection between MCC and the G protein activating region of mAChR is intriguing in Light of previous investigations relating G proteins to cancer. For example, the RAS oncogenes, which are often mutated in colorectal cancers (Vogelstein, et al., N. Engl. J. Med., vol. 319, pg. 525 (1988); Bos et al., Nature vol. 327, pg. 293 (1987)), are members of the G protein family (Bourne, et al., Nature, vol. 348, pg. 125 (1990)) as is an in vitro transformation sup¬ pressor (Noda et al., Proc. Natl. Acad. Sci. USA, vol. 86, pg. 162 (1989)) and genes mutated in hormone producing tumors (Candis et al., Nature, vol. 340, pg. 692 (1989); Lyons et al., Science, vol. 249, pg. 655 (1990)). Additionally, the gene responsible for neurofibromatosis (pre¬ sumably a tumor suppressor gene) has been shown to activate the GTPase activity of RAS (Xu et al., Cell, vol. 63, pg. 835 (1990); Martin et al., Cell, vol. 63, pg. 843 (1990); Ballester et al., Cell, vol. 63, pg. 851 (1990)). Another interesting link between G proteins and colon cancer involves the drug sulindac. This agent has been shown to inhibit the growth of benign colon tumors in patients with FAP, pre¬ sumably by virtue of its activity as a cyclooxygenase inhibitor (Waddell et al., J. Surg. Oncology 24(1), 83 (1983); Wadell, et al., Am. J. Surg., 157(1), 175 (1989); Charneau et al., Gastroenterologie Clinique at Biologique 14(2), 153 (1990)). Cyclooxygenase is required to convert arachidonic acid to prostaglandins and other biologically active molecules. G proteins are known to regulate phospholipase A 2 activity, which generates arachidonic acid from phosphplipids (Role et al., Proc. Natl. Acad. Sci. USA, vol. 84, pg. 3623 (1987); Kurachi et al., Nature, vol. 337, pg. 555 (1989)). Therefore we propose that wild-type MCC protein functions by interacting with a G protein and is involved in phospholipid metabolism.
The following are provided for exemplification purposes only and are not intended to limit the scope of the invention which has been described in broad terms above. Example 1:
This example demonstrates the detection of a somatic cell gene rearrangement occurring in chromosome 5q21 in a colorectal carcinoma.
We mapped allelie losses which occur in over 30% of sporadic cancers using restriction fragment length polymorphisms (RFLP) markers. We found that the region of common loss seems to be cen¬ tered at an RFLP detected by cosmid 5.71.
Portions of cosmid 5.71 were subcloned and used as probes to screen a panel of 150 colorectal carcinomas by Southern blot analysis. We found one tumor (T14) which contained an 11 kb EcoRl fragment in addition to the 20 kb EcoRI fragment seen in DNA from normal individuals. The 11 kb fragment was not present in DNA isolated from normal cells from the same patient (Figure 1, Panel A).
The new EcoRI fragment was cloned- , and used to probe Southern blots with DNA from tumor T14. The 11 kb clone hybridized to the abnormal 11 kb EcoRI fragment and to the normal 20 kb EcoRI fragment in the tumor as expected (Figure 1, Panel B). Moreover, the 11 kb clone detected new fragments in tumor T14 DNA upon digestion with other restriction endonucleases (including Pstl [Figure 1, Panel C ] ; Hind IE and EcoRV).
Restriction mapping and partial sequencing of the 11 kb clone showed that its left end was derived from the 20 kb EcoRI fragment which contained 5.71 sequences. The right end of the 11 kb fragment was derived from sequences which were not contiguous with the left end in normal genomic DNA. Use of a 400 bp probe from the right end of the 11 kb fragment showed that the non-contiguous sequences were also derived from chromosome 5, but from a position separated by at least 100 kb from the left end of the 11 kb EcoRI fragment. Thus a rearrangement had occurred in the tumor which resulted in the juxtaposition of sequences which were normally far apart. Example 2:
This example documents our efforts to locate a gene affected by the rearrangement found in colorectal tumor T14.
Based on the hypothesis that human genes that are expressed are evolutionarily conserved among mammalian species, we looked for genomic sequences in rat which shared homology with the 5.71 cosmid. Several subclones of the 5.71 cosmid were used in Southern blot analysis of rodent DNA. Cross-species hybridization was per¬ formed at 55 degrees as described in Vogelstein, et al., Cancer Research, vol. 47, pg. 4806 (1987), and washed for 45 minutes at 55 degrees in 45 mM sodium chloride, 2 mM sodium citrate, 0.3 mM Tris, HCl pH 7.5, 0.1% sodium dodecyl sulfate. We identified two subclones (5.71-5 and 5.71-3) that cross-hybridized under reduced stringency.
/ EcoRI fragments of T14 tumor DNA were ligated to lambda DASH vector arms (Stratagene). Following packaging and infec¬ tion of C600 E. coli cells, hybridizing clones were identified with a probe derived from 5.71 sequences. However, attempts to use these conserved sequences to detect expressed human genes by Northern blotting and cDNA library screen¬ ing of over 3 x 106 colon or brain cDNA clones were unsuccessful. Example 3:
This example demonstrates the identification of an expressed human gene near the cosmid 5.71 RFLP marker.
We sequenced parts of the human subclones demonstrating cross-species hybridization, but found it impossible to predict exons from this sequence information alone. We therefore cloned the cross-hybridizing rat fragments and determined their sequence as well. A rat genomic library in the lambda DASH vector (Stratagene) was probed with 32P-labelled 5.71-3 and 5.71-5 sequences. Cross-hybridizing restriction fragments of these phage clones were subcloned into plasmid vectors and sequenced to derive the homolo- gies shown in figure 2. Sequencing was performed with unmodified T7 polymerase as described by G. Del Sal, G. Manfioletti and C. Schneider, Biotechniques 7:514, 1989.
Through comparison of the sequences of the corresponding rat and human regions, one putative exon from subclone 5.71-3 and one from subclone 5.71-5 were identified (Figure 2). Each contained an open reading frame (ORF) that was preceded and followed by splice acceptor and donor sites that were conserved between species. The predicted ORF's from the rat and human exons were 96% identical at the amino acid level and 89% identical at the nudeotide level, with most of the nudeotide differences occurring at the third position of codons. The two putative exons are separated in genomic DNA by over 2 kb.
Primers were derived from the two putative exons. PCR per¬ formed with these primers, using cDNA as template, allows detection of putative exons if they are joined by RNA splicing within cells. Contaminating genomic DNA in the RNA preparation does not inter¬ fere with this assay, since the intervening intron(s) results in much longer PCR products from genomic DNA than that obtained from the spliced RNA.
We did not initially know the orientation of the putative exons with respect to one another and therefore designed two set of primers for the exon-eonnection scheme. One set (primers PI and P4; Figure 2) would have resulted in a PCR product if the exon in 5.71-5 was upstream of that in 5.71-3. The other set (primers P2 and P3; Figure 2) would have allowed detection of a PCR product if the exons were in the reverse orientation.
PCR was performed as described in Baker et al., Cancer Research, vol. 50, pg. 7717 (1990), using 35 cycles of: 95 degrees C for 0.5 minutes, 55 degrees C for 2 minutes, and 70 degrees C for 2 minutes. We found that only the first set (primers PI and P4) results in a PCR produet using cDNA derived from mRNA of normal human colon as template. The PCR product was exactly the size (226 bp) expected if direct splicing of the two putative exons had occurred at the splice sites identified in the human and rat genomic DNA sequences. Cloning and sequencing of the PCR product confirmed that it represented the result of a direct splice between the 5.71-5 and 5.71-3 exons. This spliced product produced an in-frame fusion of the ORF's from each exon. We concluded that these sequences did indeed represent an expressed gene, hereinafter referred to as the MCC gene for mutated in colorectal cancer. Using the exon-connection strategy, we found that MCC was expressed in most normal tissues of the rat (e.g., colon, brain, stomach, lung, liver, kid¬ ney, bladder, heart). Example 4:
This example demonstrates the isolation and sequencing of the human MCC cDNA from brain.
The PCR product amplified using human cDNA as a template was then labelled and used as a probe to screen a cDNA library from normal human brain. Brain was chosen because the exon-connection assay suggested that MCC was expressed at high levels in this tissue. The cDNA library was constructed from human brain mRNA as described in U. Gubler and B.J. Hoffman, Gene 25, 263 (1983) and the Lambda Zap vector (Stratagene). 1.5 x 106 plaques were screened with the PCR product connecting the 5.71-3 and 5.71-5 exons (see Figure 2.)
Three clones were identified in the 1.5 x 106 plaques in the initial screen. The ends of these three clones were then used to
SUBSTITUTE SHEET re-screen the library, and a series of seven overlapping cDNA clones were finally isolated and ordered. Sequence analysis of these clones indicated that they encompassed 4,180 bp of MCC mRNA and con¬ tained an ORF of 2,511 bp (Figure 3). The first methionine of the ORF (nudeotide 220) was preceded by in frame stop codons upstream and conformed reasonably well to the consensus initiation site defined by Kozak (Nucleic Acids Research, vol. 15, pg. 8125 (1987)). If trans¬ lation initiation occurs at this methionine, the sequence predicts an 829 amino acid product (93kd) encoded from nudeotide 220 to 2707. The ORF was surrounded by at least 200 bp of 5' untranslated sequence and 1450 bp of 3' untranslated sequence. There was no evi¬ dence of a polyadenylylation tract at the 3' end of any clone. cDNA probes detected RNAs of several seizes (3-10 kb) on Northern blots; we do not know whether these other transcripts represent alterna¬ tively spliced forms of the MCC gene or related genes from other loci.
Searches of nudeotide databases (EMBL version 25, Genbank version 66) indicated that this sequence has not been previously reported. Searches of amino acid databases (P.I.R. version 25, SWISS-Protein version 16) with the predicted MCC protein (829 amino acids) also failed to reveal any extensive homologies. However, we noted a 19 amino acid region of homology between MCC and the G-protein-coupled muscarinic acetylcholine receptor of humans and pigs. Example 5:
This example demonstrates that somatic mutations occur within the MCC gene in colorectal carcinoma tissue.
When the sequences of MCC were compared with those of genomic clones from tumor T14 it was found that the boundary of the rearrangement in this tumor was within the MCC gene, occurring in the intron just distal to the exon containing nudeotides 534 to 676. As noted above, the novel 11 kb restriction fragment represented the joining of sequences on chromosome 5 normally separated by more than 100 kb. This 100 kb stretch contained several exons of the MCC gene. Thus, the MCC gene was disrupted by a genetic alteration which removed several exons from the rearranged MCC gene in this tumor.
To search for other more subtle genetic alterations of MCC, we employed the polymerase chain reaction to amplify exons of the MCC gene from colorectal cancers. These sequences were then analyzed for mutations by an RNase protection assay which was modified to allow rapid testing of multiple samples. In brief, the sequence of an exon and surrounding intron was determined and used to design prim¬ ers for the amplification of the exon and surrounding splice sites. The exon was then amplified from tumor DNA using PCR.
The sequences of exon boundaries were derived following the screening of human genomic DNA libraries with MCC cDNA probes. Positively hybridizing clones were isolated and small fragments (0.2-3kb) subcloned and sequenced. Primers for amplifying the exons were chosen outside of the splice sites and were as follows: 5'-GAATTCATCAGCACTTCT-3* (SEQ ID NO:3) and
5'-CAGCTCCAAGATGGAGGG-3' (SEQ ID NO:4) for the exon contain¬ ing nudeotides 391 to 533, 5'-GGCCCCATGTGCTTTGTT-3' (SEQ ID NO:5) and 5'-AGAGGGACTCTGGAGACA-3* (SEQ ID NO:6) for the exon containing nudeotides 1575 to 1678,
5'-ATGTTGATTAATCCGTTGGC-3' (SEQ ID NO:7) and δ'-ACCCCAGAGCAGAAGGCT-S' (SEQ ID NO: 8) for the exon con- ■ ta ing nudeotides 1679-1862, 5'-GGCCTAACTGGAATGTGT-3' (SEQ ID NO: 9) and 5*-GCCCAGATAAACACCAGC-3* (SEQ ID NO:10) for the exon containing nudeotides 2305 to 2405. PCR was carried out as described above.
The resulting PCR products were hybridized to in vitro gener¬ ated RNA probes representing normal MCC sequences. The hybrids were digested with RNase A, which can cleave at single base pair mismatches within DNA-RNA hybrids, and these cleavage products visualized following denaturing gel electrophoresis. Two separate RNase protection analyses were performed for each exon, one with the sense and one with the antisense strand as labeled transcript. Under these conditions approximately 50% of all point mutations are detectable. R.M. Myers and T. Maniatis, Cold Spring Harbor Symposia on Quantitative Biology, 51, 275 (1986). The RNAse protection assay was performed as described by Winter et al., Proc. Natl. Acad. Sci. USA, vol. 82, pg. 7575 (1985) with the following modifications: Hybridizations were carried out in 9 ul of hybridization solution containing 1 ul of the appropriate PCR reac¬ tion and 3 P labeled transcript (200,000 dpm) for 2 hours at 50 degrees C. RNase treatment was initiated by addition of 90 ul of RNase solu¬ tion (0.2 M NaCl, 0.1 M LiCl, 20 mM Tris-HCl, pH 7.5, ImM EDTA, 25 ug/ml RNase A) and incubated 1 hour at 37 degrees C. RNase treat¬ ment was terminated by the addition of proteinase K solution (5 mg/ml proteinase K in 10% SDS) and incubated 1 hour at 37 degrees C. The solution was then extracted one time with PC 9 (3 parts phenol and 4 parts chloroform equilibrated with 2 parts 0.5 M Tris-HCl, pH 9.0, 10 mM EDTA, 10 mM NaCl) and 20 ul of the aqueous phase was collected and combined wtih 20 ul of loading buffer (0.3% W/V xylene cyanol, 0.3% W/V bromophenol blue in formamide). The samples were then heated at 94 degrees C for 4 minutes and loaded directly on a denaturing polyacrylamide gel. Two separate assays were performed for each exon, one with each strand as labeled transcript.
The first exon (containing nudeotides 391 to 533) of four tested showed no variants among 100 colorectal tumors tested. Analysis of the exon containing nudeotides 1575 to 1678 identified five tumors with identical variations in their RNase protection pattern. Cloning and sequencing of the variant PCR product from two of the five tumors indicated that it resulted from a C to T transition at nudeotide 1676 which resulted in a coding change from proline to leucine. This variant presumably represents a polymorphism, as it was found in five individuals and was present in DNA from the normal tissue of two of the five patients whose tumors showed the variant (the other three were not tested).
Analysis of a third exon (containing nudeotides 2305 to 2405) identified a single tumor (T91) with a unique RNase protection pat¬ tern. This abnormal RNase protection pattern was not seen in DNA isolated from normal tissue from the same individual (Figure 4). This indicates that the altered RNase protection pattern was the result of a somatic mutation. Cloning and sequencing of the T91 tumor PCR product indicated that it had a C to T transition at nudeotide 2312 that resulted in a coding change from alanine to valine. Although this is a relatively conservative amino acid substitution, the identical amino acid change has been shown to inactivate the p53 tumor sup¬ pressor gene. S.J. Baker et al., Science, vol. 244, pg. 217 (1989); S.J. Baker et al., Science, vol. 249, pg. 912 (1990).
Analysis of a fourth exon (containing nudeotides 1679 to 1862) identified a single tumor (T35) with a unique RNase protection pat¬ tern. Examination of DNA isolated from normal tissue of the same individual indicated that this altered RNase protection pattern was also the result of a somatic mutation (Figure 4). Cloning and sequenc¬ ing of the T35 PCR product indicated that it had a G to A transition at nudeotide 1736 resulting in a coding change from arginine to glutamine.
SEQUENCE LISTING
(1) GENERAL INFORMATION:
(i) APPLICANT: Vogelstein, Bert
Kinzler, Kenneth W. White, Raymond Nakamura, Yusu e
(ii) TITLE OF INVENTION: Gene Mutated in Colorectal Cancer of Humans
(iii) NUMBER OF SEQUENCES: 19
(iv) CORRESPONDENCE ADDRESS:
(A) ADDRESSEE: Banner, Birch et al.
(B) STREET: 1001 G Street
(C) CITY: Washington
(D) STATE: D.C.
(E) COUNTRY: U.S.A.
(F) ZIP: 20001-4597
(V) COMPUTER READABLE FORM:
(A) MEDIUM TYPE: Floppy disk
(B) COMPUTER: IBM PC compatible
(C) OPERATING SYSTEM: PC-DOS/MS-DOS
(D) SOFTWARE: Patentln Release #1.0, Version #1.25
(Vi) CURRENT APPLICATION DATA:
(A) APPLICATION NUMBER:
(B) FILING DATE: 13-MAR-1991
(C) CLASSIFICATION:
(viii) ATTORNEY/AGENT INFORMATION:
(A) NAME: Kagan, Sarah A.
(B) REGISTRATION NUMBER: 32,141 - 24 -
(C) REFERENCE/DOCKET NUMBER: 1107.33981
(ix) TELECOMMUNICATION INFORMATION: (A) TELEPHONE: 202-508-9100
(2) INFORMATION FOR SEQ ID NO:l:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 4181 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: cDNA
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Homo sapiens
(viii) POSITION IN GENOME:
(A) CHROMOSOME/SEGMENT: 5q21
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:l:
CCTCCTGCAG CAATGGCTCG TCCGTGAAAC GCGAGCCACG GCTGCTCTTT TTAAGAGTGC 60
CTGCATCCTC CGTTTGCGCT TCGCAACTGT CCTGGGTGAA AATGGCTGTC TAGACTAAAA 120
TGTGGCAGAA GGGACCAAGC AGTGGATATT GAGCCTGTGA AGTCCAACTC TTAAGCTCCG 180
AGACCTGGGG GACTGAGAGC CCAGCTCTGA AAAGTGCATC ATGAATTCCG GAGTTGCCAT 240
GAAATATGGA AACGACTCCT CGGCCGAGCT GAGTGAGCTC CATTCAGCAG CCCTGGCATC 300
ACTAAAGGGA GATATAGTGG AACTTAATAA ACGTCTCCAG CAAACAGAGA GGGAACGGGA 360 CCTTCTGGAA AAGAAATTGG CCAAGGCACA GTGCGAGCAG TCCCACCTCA TGAGAGAGCA 420
TGAGGATGTC CAGGAGCGAA CGACGCTTCG CTATGAGGAA CGCATCACAG AGCTCCACAG 480
CGTCATTGCG GAGCTCAACA AGAAGATAGA CCGTCTGCAA GGCACCACCA TCAGGGAGGA 540
AGATGAGTAC TCAGAACTGC GATCAGAACT CAGCCAGAGC CAACACGAGG TCAACGAGGA 600
CTCTCGAAGC ATGGACCAAG ACCAGACCTC TGTCTCTATC CCCGAAAACC AGTCTACCAT 660
GGTTACTGCT GACATGGACA ACTGCAGTGA CCTGAACTCA GAACTGCAGA GGGTGCTGAC 720
AGGGCTGGAG AATGTTGTCT GCGGCAGGAA GAAGAGCAGC TGCAGCCTCT CCGTGGCCGA 780
GGTGGACAGG CACATTGAGC AGCTCACCAC AGCCAGCGAG CACTGTGACC TGGCTATTAA 840
GACAGTCGAG GAGATTGAGG GGGTGCTTGG CCGGGACCTG TATCCCAACC TGGCTGAAGA 900
GAGGTCTCGG TGGGAGAAGG AGCTGGCTGG GCTGAGGGAA GAGAATGAGA GCCTGACTGC 960
CATGCTGTGC AGCAAAGAGG AAGAACTGAA CCGGACTAAG GCCACCATGA ATGCCATCCG 1020
GGAAGAGCGG GACCGGCTCC GGAGGCGGGT CAGAGAGCTT CAAACTCGAC TACAGAGCGT 1080
GCAGGCCACA GGTCCCTCCA GCCCTGGCCG CCTCACTTCC ACCAACCGCC CGATTAACCC 1140
CAGCACTGGG GAGCTGAGCA CAAGCAGCAG CAGCAATGAC ATTCCCATCG CCAAGATTGC 1200
TGAGAGGGTG AAGCTATCAA AGACAAGGTC CGAATCGTCA TCATCTGATC GGCCAGTCCT 1260
GGGCTCAGAA ATCAGTAGCA TAGGGGTATC CAGCAGTGTG GCTGAACACC TGGCCCACTC 1320
ACTTCAGGAC TGCTCCAATA TCCAAGAGAT TTTCCAAACA CTCTACTCAC ACGGATCTGC 1380
CATCTCAGAA AGCAAGATTA GAGAGTTTGA GGTGGAAACA GAACGGCTGA ATAGCCGGAT 1440
TGAGCACCTC AAATCCCAAA ATGACCTCCT GACCATAACC TTGGAGGAAT GTAAAAGCAA 1500
TGCTGAGAGG ATGAGCATGC TGGTGGGAAA ATACGAATCC AATGCCACAG CGCTGAGGCT 1560
GGCCTTGCAG TACAGCGAGC AGTGCATCGA AGCCTACGAA CTCCTCCTGG CGCTGGCAGA 1620 - 26 -
GAGTGAGCAG AGCCTCATCC TGGGGCAGTT CCGAGCGGCG GGCGTGGGGT CCTCCCCTGG 1680
AGACCAGTCG GGGGATGAAA ACATCACTCA GATGCTCAAG CGAGCTCATG ACTGCCGGAA 1740
GACAGCTGAG AACGCTGCCA AGGCCCTGCT CATGAAGCTG GACGGCAGCT GTGGGGGAGC 1800
CTTTGCCGTG GCCGGCTGCA GCGTGCAGCC CTGGGAGAGC CTTTCCTCCA ACAGCCACAC 1860
CAGCACAACC AGCTCCACAG CCAGTAGTTG CGACACCGAG TTCACTAAAG AAGACGAGCA 1920
GAGGCTGAAG GATTATATCC AGCAGCTCAA GAATGACAGG GCTGCGGTCA AGCTGACCAT 1980
GCTGGAGCTG GAAAGCATCC ACATCGATCC TCTCAGCTAT GACGTCAAGC CTCGGGGAGA 2040
CAGCCAGAGG CTGGATCTGG AAAACGCAGT GCTTATGCAG GAGCTCATGG CCATGAAGGA 2100
GGAGATGGCC GAGTTGAAGG CCCAGCTCTA CCTACTGGAG AAAGAGAAGA AGGCCCTGGA 2160
GCTGAAGCTG AGCACGCGGG AGGCCCAGGA GCAGGCCTAC CTGGTGCACA TTGAGCACCT 2220
GAAGTCCGAG GTGGAGGAGC AGAAGGAGCA GCGGATGCGA TCCCTCAGCT CCACCAGCAG 2280
CGGCAGCAAA GATAAACCTG GCAAGGAGTG TGCTGATGCT GCCTCCCCAG CTCTGTCCCT 2340
AGCTGAACTC AGGACAACGT GCAGCGAGAA TGAGCTGGCT GCGGAGTTCA CCAACGCCAT 2400
TCGTCGAGAA AAGAAGTTGA AGGCCAGAGT TCAAGAGCTG GTGAGTGCCT TGGAGAGACT 2460
CACCAAGAGC AGTGAAATCC GACATCAGCA ATCTGCAGAG TTCGTGAATG ATCTAAAGCG 2520
GGCCAACAGC AACCTGGTGG CTGCCTATGA GAAAGCAAAG AAAAAGCATC AAAACAAACT 2580
GAAGAAGTTA GAGTCGCAGA TGATGGCCAT GGTGGAGAGA CATGAGACCC AAGTGAGGAT 2640
GCTCAAGCAA AGAATAGCTC TGCTAGAGGA GGAGAACTCC AGGCCACACA CCAATGAAAC 2700
TTCGCTTTAA TCAGCACTCA CGCACCGGAG TTCTGCCCAT GGGAAGTAAA CTGCAGCAGG 2760
CCACTGGGGA CAGAAGGGCC CATGTACTTG TTGGGAGGAG GAGGAAAGGG AAGGCTGGCA 2820
GGTAGGTCGG CACTTGGACA ATGGAGTGCC CCAACTCAAC CCTTGGGGTG ACTGGCCATG 2880 GTGACATTGT GGACTGTATC CAGAGGTGCC CGCTCTTCCC TCCTGGGCCC ACAACAGCGT 2940
GTAAACACAT GTTCTGTGCC TGCTCAGCAG AGCCTCGTTT CTGCTTTCAG CACTCACTCT 3000
CCCCCTCCTC TTCTGGTCTG GCGGCTGTGC ATCAGTGGGA TCCCAGACAT TTGTTTCTGT 3060
AAGATTTTCC ATTGTATCCT CTTTTTGGTA GATGCTGGGC TCATCTTCTA GAATCTCGTT 3120
TCTCCTCTTT CCTCCTGCTT CATGGGAAAA CAGACCTGTG TGTGCCTCCA GCATTTAAAA 3180
GGACTGCTGA TTTGTTTACT ACAGCAAGGC TTTGGTTTCC AAGTCCCGGG TCTCAACTTT 3240
AAGATAGAGG CGGCCATAAG AGGTGATCTC TGGGAGTTAT AGGTCATGGG AAGAGCGTAG 3300
ACAGGTGTTA CTTACAGTCC CAGATACACT AAAGTTACAA ACAGACCACC ACCAGGACTG 3360
TGCCTGAACA ATTTTGTATT GAGAGAATAA AAACTTCCTT CΛATCTTCAT TTTGGAGGCA 3420
GGGCTGGGAA GGGAGCGCTC TCTTGATTCT GGGATTTCTC CCTCTCAGTG GAGCCTTATT 3480
AATATCCAAG ACTTAGAGCT GGGAATCTTT TTGATACCTG TAGTGGAACT AAAATTCTGT 3540
CAGGGGTTTC TTCAAGAGCT GAGAAACATT ATTAGCACTT CCCGCCCCAG GGCACTACAT 3600
AATTGCTGTT CTGCTGAATC AAATCTCTTC CACATGGGTG CATTTGTAGC TCTGGACCTG 3660
TCTCTACCTA AGGACAAGAC ACTGAGGAGA TACTGAACAT TTTGCAAAAC TTATCACGCC 3720
TACTTAAGAG TGCTGTGTAA CCCCCAGTTC AAGACTTAGC .TCCTGTTGTC ATGACGGGGA 3780
CAGAGTGAGG GAATGGTAGT TAAGGCTTCT TTTTTGCCCC CAGATACATG GTGATGGTTA 3840
GCATATGGTG CTTAAAAGGT TAAATTTCAA GCAAAATGCT TACAGGGCTA GGCAGTACCA 3900
AAGTAACTGA ATTATTTCAG GAAGGTCTTC AATCTTAAAA CAAATTCATT ATTCTTTTTC 3960
AGTTTTACCT CTTCTCTCTC AGTTCTACAC TGATACACTT GAAGGACCAT TTACTGTTTT 4020
TTTCTGTAGC ACCAGAGAAT CCATCCAAAG TTCCCTATGA AAAATGTGTT CCATTGCCAT 4080
AGCTGACTAC AAATTAAAGT TGAGGAGGTT TCTGCATAGA GTCTTTATGT CCATAAGCTA 4140 CGGGTAGGTC TATTTTCAGA GCATGATACA AATTCCACAG G 4181
(2) INFORMATION FOR SEQ ID NO:2:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 amino acids
(B) TYPE: amino acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Homo sapiens
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:2:
Met Asn Ser Gly Val Ala Met Lys Tyr Gly Asn Asp Ser Ser Ala Glu 1 5 10 15
Leu Ser Glu Leu His Ser Ala Ala Leu Ala Ser Leu Lys Gly Asp lie 20 25 30
Val Glu Leu Asn Lys Arg Leu Gin Gin Thr Glu Arg Glu Arg Asp Leu 35 40 45
Leu Glu Lys Lys Leu Ala Lys Ala Gin Cys Glu Gin Ser His Leu Met 50 55 60
Arg Glu His Glu Asp Val Gin Glu Arg Thr Thr Leu Arg Tyr Glu Glu 65 70 75 80
Arg lie Thr Glu Leu His Ser Val lie Ala Glu Leu Asn Lys Lys lie 85 90 95 Asp Arg Leu Gin Gly Thr Thr lie Arg Glu Glu Asp Glu Tyr Ser Glu 100 105 110
Leu Arg Ser Glu Leu Ser Gin Ser Gin His Glu Val Asn Glu Asp Ser 115 120 125
Arg Ser Met Asp Gin Asp Gin Thr Ser Val Ser lie Pro Glu Asn Gin 130 135 140
Ser Thr Met Val Thr Ala Asp Met Asp Asn Cys Ser Asp Leu Asn Ser 145 150 155 160
Glu Leu Gin Arg Val Leu Thr Gly Leu Glu Asn Val Val Cys Gly Arg 165 170 175
Lys Lys Ser Ser Cys Ser Leu Ser Val Ala Glu Val Asp Arg His lie 180 185 190
Glu Gin Leu Thr Thr Ala Ser Glu His Cys Asp Leu Ala lie Lys Thr 195 200 205
Val Glu Glu He Glu Gly Val Leu Gly Arg Asp Leu Tyr Pro Asn Leu 210 215 220
Ala Glu Glu Arg Ser Arg Trp Glu Lys Glu Leu Ala Gly Leu Arg Glu 225 230 235 240
Glu Asn Glu Ser Leu Thr Ala Met Leu Cys Ser Lys Glu Glu Glu Leu 245 250 255
Asn Arg Thr Lys Ala Thr Met Asn Ala He Arg Glu Glu Arg Asp Arg 260 265 270
Leu Arg Arg Arg Val Arg Glu Leu Gin Thr Arg Leu Gin Ser Val Gin 275 280 285
Ala Thr Gly Pro Ser Ser Pro Gly Arg Leu Thr Ser Thr Asn Arg Pro 290 295 300 Ile Asn Pro Ser Thr Gly Glu Leu Ser Thr Ser Ser Ser Ser Asn Asp 305 310 315 320
He Pro He Ala Lys He Ala Glu Arg Val Lys Leu Ser Lys Thr Arg 325 330 335
Ser Glu Ser Ser Ser Ser Asp Arg Pro Val Leu Gly Ser Glu He Ser 340 345 350
Ser He Gly Val Ser Ser Ser Val Ala Glu His Leu Ala His Ser Leu 355 360 365
Gin Asp Cys Ser Asn He Gin Glu He Phe Gin Thr Leu Tyr Ser His 370 375 380
Gly Ser Ala He Ser Glu Ser Lys He Arg Glu Phe Glu Val Glu Thr 385 390 395 400
Glu Arg Leu Asn Ser Arg He Glu His Leu Lys Ser Gin Asn Asp Leu 405 410 415
Leu Thr He Thr Leu Glu Glu Cys Lys Ser Asn Ala Glu Arg Met Ser 420 425 430
Met Leu Val Gly Lys Tyr Glu Ser Asn Ala Thr Ala Leu Arg Leu Ala 435 440 445
Leu Gin Tyr Ser Glu Gin Cys He Glu Ala Tyr Glu Leu Leu Leu Ala 450 455 460
Leu Ala Glu Ser Glu Gin Ser Leu He Leu Gly Gin Phe Arg Ala Ala 465 470 475 480
Gly Val Gly Ser Ser Pro Gly Asp Gin Ser Gly Asp Glu Asn He Thr 485 490 495
Gin Met Leu Lys Arg Ala His Asp Cys Arg Lys Thr Ala Glu Asn Ala 500 505 510 Ala Lys Ala Leu Leu Met Lys Leu Asp Gly Ser Cys Gly Gly Ala Phe 515 520 525
Ala Val Ala Gly Cys Ser Val Gin Pro Trp Glu Ser Leu Ser Ser Asn 530 535 540
Ser His Thr Ser Thr Thr Ser Ser Thr Ala Ser Ser Cys Asp Thr Glu 545 550 555 560
Phe Thr Lys Glu Asp Glu Gin Arg Leu Lys Asp Tyr He Gin Gin Leu 565 570 575
Lys Asn Asp Arg Ala Ala Val Lys Leu Thr Met Leu Glu Leu Glu Ser 580 585 590
He His He Asp Pro Leu Ser Tyr Asp Val Lys Pro Arg Gly Asp Ser 595 600 605
Gin Arg Leu Asp Leu Glu Asn Ala Val Leu Met Gin Glu Leu Met Ala 610 615 620
Met Lys Glu Glu Met Ala Glu Leu Lys Ala Gin Leu Tyr Leu Leu Glu 625 630 635 640
Lys Glu Lys Lys Ala Leu Glu Leu Lys Leu Ser Thr Arg Glu Ala Gin 645 650 655
Glu Gin Ala Tyr Leu Val His He Glu His Leu Lys Ser Glu Val Glu 660 665 670
Glu Gin Lys Glu Gin Arg Met Arg Ser Leu Ser Ser Thr Ser Ser Gly 675 680 685
Ser Lys Asp Lys Pro Gly Lys Glu Cys Ala Asp Ala Ala Ser Pro Ala 690 695 700
Leu Ser Leu Ala Glu Leu Arg Thr Thr Cys Ser Glu Asn Glu Leu Ala 705 710 715 720 Ala Glu Phe Thr Asn Ala He Arg Arg Glu Lys Lys Leu Lys Ala Arg 725 730 735
Val Gin Glu Leu Val Ser Ala Leu Glu Arg Leu Thr Lys Ser Ser Glu 740 745 750
He Arg His Gin Gin Ser Ala Glu Phe Val Asn Asp Leu Lys Arg Ala 755 760 765
Asn Ser Asn Leu Val Ala Ala Tyr Glu Lys Ala Lys Lys Lys His Gin 770 775 780
Asn Lys Leu Lys Lys Leu Glu Ser Gin Met Met Ala Met Val Glu Arg 785 790 795 800
His Glu Thr Gin Val Arg Met Leu Lys Gin Arg He Ala Leu Leu Glu 805 810 815
Glu Glu Asn Ser Arg Pro His Thr Asn Glu Thr Ser Leu 820 825
(2) INFORMATION FOR SEQ ID NO:3:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 18 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(Vi) ORIGINAL SOURCE:
(A) ORGANISM: Homo sapiens
(viii) POSITION IN GENOME:
SUBSTITUTESH (A) CHROMOSOME/SEGMENT: 5q21
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:3:
GAATTCATCA GCACTTCT 18
(2) INFORMATION FOR SEQ ID NO:4:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 18 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(Vi) ORIGINAL SOURCE:
(A) ORGANISM: Homo sapiens
(viii) POSITION IN GENOME:
(A) CHROMOSOME/SEGMENT: 5q21
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:4:
CAGCTCCAAG ATGGAGGG 18
(2) INFORMATION FOR SEQ ID NO:5:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 18 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Homo sapiens
(viii) POSITION IN GENOME:
(A) CHROMOSOME/SEGMENT: 5q21
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:5:
GGCCCCATGT GCTTTGTT 18
(2) INFORMATION FOR SEQ ID NO:6:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 18 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Homo sapiens
(viii) POSITION IN GENOME:
(A) CHROMOSOME/SEGMENT: 5q21 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:6:
AGAGGGACTC TGGAGACA 18
(2) INFORMATION FOR SEQ ID NO:7:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 20 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Homo sapiens
(viii) POSITION IN GENOME:
(A) CHROMOSOME/SEGMENT: 5q21
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:7:
ATGTTGATTA ATCCGTTGGC 20
(2) INFORMATION FOR SEQ ID NO:8:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 18 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Homo sapiens
(viii) POSITION IN GENOME:
(A) CHROMOSOME/SEGMENT: 5q21
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:8:
ACCCCAGAGC AGAAGGCT 18
(2) INFORMATION FOR SEQ ID NO:9:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 18 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Homo sapiens
(Viii) POSITION IN GENOME:
(A) CHROMOSOME/SEGMENT: 5q21
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:9:
GGCCTAACTG GAATGTGT 18
(2) INFORMATION FOR SEQ ID NO:10: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 18 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Homo sapiens
(viii) POSITION IN GENOME:
(A) CHROMOSOME/SEGMENT: 5q21
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:10:
GCCCAGATAA ACACCAGC 18
(2) INFORMATION FOR SEQ ID NO:11:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 24 amino acids
(B) TYPE: amino acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: peptide
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(v) FRAGMENT TYPE: internal
(vi) ORIGINAL SOURCE: (A) ORGANISM: Homo sapiens
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:11:
Leu Tyr Trp Arg He Tyr Lys Glu Thr Glu Lys Arg Thr Lys Glu Leu 1 5 10 15
Ala Gly Leu Gin Ala Ser Gly Thr 20
(2) INFORMATION FOR SEQ ID NO:12:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 206 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Homo sapiens
(ix) FEATURE:
(A) NAME/KEY: CDS
(B) LOCATION: 32..172
(ix) FEATURE:
(A) NAME/KEY: exon
(B) LOCATION: 32..174 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:12:
CAGCACTTCT GTCCTTTTCC CTTATTCCCA G TGC GAG CAG TCC CAC CTC ATG 52
Cys Glu Gin Ser His Leu Met 1 5
AGA GAG CAT GAG GAT GTC CAG GAG CGA ACG ACG CTT CGC TAT GAG GAA 100 Arg Glu His Glu Asp Val Gin Glu Arg Thr Thr Leu Arg Tyr Glu Glu 10 15 20
CGC ATC ACA GAG CTC CAC AGC GTC ATT GCG GAG CTC AAC AAG AAG ATA 148 Arg He Thr Glu Leu His Ser Val He Ala Glu Leu Asn Lys Lys He 25 30 35
GAC CGT CTG CAA GGC ACC ACC ATC AGGTACGCGG CTCCATTCGG CTTTTACTCT 202 Asp Arg Leu Gin Gly Thr Thr He 40 45
GCCC 206
(2) INFORMATION FOR SEQ ID NO:13:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 47 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:13:
Cys Glu Gin Ser His Leu Met Arg Glu His Glu Asp Val Gin Glu Arg 1 5 10 15
Thr Thr Leu Arg Tyr Glu Glu Arg He Thr Glu Leu His Ser Val He 20 25 30 Ala Glu Leu Asn Lys Lys He Asp Arg Leu Gin Gly Thr Thr He 35 40 45
(2) INFORMATION FOR SEQ ID NO:14:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 206 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Rattus rattus
(ix) FEATURE:
(A) NAME/KEY: exon
(B) LOCATION: 32..174
(ix) FEATURE:
(A) NAME/KEY: CDS
(B) LOCATION: 32..172
( i) SEQUENCE DESCRIPTION: SEQ ID NO:14:
TCCGTCTTCT CCTCTTTGTT CTTGGCCCTA G TGT GAG CAG TCA CAC CTC ATG 52
Cys Glu Gin Ser His Leu Met 1 5
AGA GAG CAT GAA GAT GTT CAG GAA CGC ACG ACA CTC CGC TAT GAG GAG 100 Arg Glu His Glu Asp Val Gin Glu Arg Thr Thr Leu Arg Tyr Glu Glu 10 15 ■ 20 CGC ATC ACA GAG CTC CAC AGC ATC ATT GCA GAA CTC AAC AAG AAG ATA 148 Arg He Thr Glu Leu His Ser He He Ala Glu Leu Asn Lys Lys He 25 30 35
GAC CGC TTG CAA GGT ACC ACC ATC AGGTATGGCT GCTATTTAAC CTGTGCTGGT 202 Asp Arg Leu Gin Gly Thr Thr He 40 45
CCTT 206
(2) INFORMATION FOR SEQ ID NO:15:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 47 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:15:
Cys Glu Gin Ser His Leu Met Arg Glu His Glu Asp Val Gin Glu Arg 1 5 10 15
Thr Thr Leu Arg Tyr Glu Glu Arg He Thr Glu Leu His Ser He He 20 25 30
Ala Glu Leu Asn Lys Lys He Asp Arg Leu Gin Gly Thr Thr He 35 40 45
(2) INFORMATION FOR SEQ ID NO:16:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 208 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: linear • (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Homo sapiens
(viii) POSITION IN GENOME:
(A) CHROMOSOME/SEGMENT: 5q21
(ix) FEATURE:
(A) NAME/KEY: CDS
(B) LOCATION: 35..175
(ix) FEATURE:
(A) NAME/KEY: exon
(B) LOCATION: 34..176
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:16:
TGTTAGTGGT TGCCAATTCT CCTTTTTTCT CAGG GAG GAA GAT GAG TAC TCA 52
Glu Glu Asp Glu Tyr Ser 1 5
GAA CTG CGA TCA GAA CTC AGC CAG AGC CAA CAC GAG GTC AAC GAG GAC 100 Glu Leu Arg Ser Glu Leu Ser Gin Ser Gin His Glu Val Asn Glu Asp 10 15 20
TCT CGA AGC ATG GAC CAA GAC CAG ACC TCT GTC TCT ATC CCC GAA AAC 148 Ser Arg Ser Met Asp Gin Asp Gin Thr Ser Val Ser He Pro Glu Asn 25 30 35
CAG TCT ACC ATG GTT ACT GCT GAC ATG GGTGAGTCTG CCTGCCCTTG 195
Gin Ser Thr Met Val Thr Ala Asp Met 40 45 CCACCAAGCC AGA 208
(2) INFORMATION FOR SEQ ID NO:17:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 47 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:17:
Glu Glu Asp Glu Tyr Ser Glu .Leu Arg Ser Glu Leu Ser Gin Ser Gin 1 5 10 15
His Glu Val Asn Glu Asp Ser Arg Ser Met Asp Gin Asp Gin Thr Ser 20 25 30
Val Ser He Pro Glu Asn Gin Ser Thr Met Val Thr Ala Asp Met 35 40 45
(2) INFORMATION FOR SEQ ID NO:18:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 208 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Rattus rattus (ix) FEATURE:
(A) NAME/KEY: exon
(B) LOCATION: 34..176
(ix) FEATURE:
(A) NAME/KEY: CDS
(B) LOCATION: 35..175
( i) SEQUENCE DESCRIPTION: SEQ ID NO:18:
CACTCAATGG TGAGTGGCTC TCTTTTTTTG CAGG GAG GAA GAT GAG TAC TCA 52
Glu Glu Asp Glu Tyr Ser 1 5
GAA CTT CGG TCA GAG CTC AGC CAG AGT CAA CAA GAG GTC AAT GAA GAC 100 Glu Leu Arg Ser Glu Leu Ser Gin Ser Gin Gin Glu Val Asn Glu Asp 10 15 20
TCC AGA AGT GTG GAC CAA GAC CAG ACC TCT GTG TCC ATC CCT GAG AAC 148 Ser Arg Ser Val Asp Gin Asp Gin Thr Ser Val Ser He Pro Glu Asn 25 30 35
CAG TCT ACT ATG GTC ACT GCT GAC ATG GGTGAGTCTT CCCAGGCCTC 195 Gin Ser Thr Met Val Thr Ala Asp Met 40 45
CTGCTTAGTT TCT 208
(2) INFORMATION FOR SEQ ID NO:19:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 47 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (xi) SEQUENCE DESCRIPTION: SEQ ID NO:19:
Glu Glu Asp Glu Tyr Ser Glu Leu Arg Ser Glu Leu Ser Gin Ser Gin 1 5 10 15
Gin Glu Val Asn Glu Asp Ser Arg Ser Val Asp Gin Asp Gin Thr Ser 20 25 30
Val Ser He Pro Glu Asn Gin Ser Thr Met Val Thr Ala Asp Met 35 40 45

Claims

C AIMS
1. A method of diagnosing or prognosing a neoplastic tissue of a human, comprising: detecting alteration of wild-type MCC gene coding sequences or their expression products in a tumor tissue isolated from a human, said alteration indicating neoplasia of the tissue.
2. The method of claim 1 wherein the expression products are mRNA molecules.
3. The method of claim 2 wherein the alteration of wild-type MCC mRNA is detected by hybridization of mRNA from said tissue to an MCC gene probe.
4. The method of claim 1 wherein alteration of wild-type MCC gene coding sequences is detected by hybridization of an MCC gene coding sequence probe to genomic DNA isolated from said tissue.
5. The method of claim 4 further comprising: subjecting genomic DNA isolated from a non-neoplastic tissue of the human to Southern hybridization with the MCC gene coding sequence probe; and comparing the hybridizations of the MCC gene probe to said tumor and non-neoplastic tissues.
6. The method of claim 4 wherein the MCC gene probe detects a restriction fragment length polymorphism.
7. The method of claim 1 wherein the alteration of wild-type MCC gene coding sequences is detected by determining the sequence of all or part of an MCC gene in said tissue using a polymerase chain reaction, deviations in the MCC sequence deter¬ mined from that of the sequence shown in SEQ ID NO: 1 indicating neoplasia.
8. The method of claim 1 wherein the alteration of wild- type MCC gene coding sequences is detected by identifying a mis¬ match between molecules (1) an MCC gene or MCC mRNA isolated from said tissue and (2) a nucleic acid probe complementary to the human wild-type MCC gene coding sequence, when molecules (1) and (2) are hybridized to each other to form a duplex.
9. The method of claim 4 wherein the MCC gene probe hybridizes to an exon selected from the group consisting of: (1) nudeotides 2305 to 2405; and (2) nudeotides 1679-1862.
10. The method of claim 1 wherein the alteration of wild- type MCC gene coding sequences is detected by amplification of MCC gene sequences in said tissue and hybridization of the amplified MCC sequences to nucleic acid probes which comprise MCC sequences.
11. The method of claim 1 wherein the alteration of wild-type MCC gene coding sequences is detected by molecular clon¬ ing of the MCC genes in said tissue and sequencing all or part of the cloned MCC gene.
12. The method of claim 1 wherein the detection of alter¬ ation of wild-type MCC gene coding sequences comprises screening for a deletion mutation.
13. The method of claim 1 wherein the detection of alter¬ ation of wild-type MCC gene coding sequences comprises screening for a point mutation.
14. The method of claim 1 wherein the detection of alter¬ ation of wild-type MCC gene coding sequences comprises screening for an insertion mutation.
15. The method of claim 1 wherein the tissue isolated from a human is from colonic mucosa.
16. The method of claim 1 wherein the expression products are protein molecules.
17. The method of claim 16 wherein the alteration of wild-type MCC protein is detected by immunoblotting.
18. The method of claim 16 wherein the alteration of wild-type MCC protein is detected by immunocytochemistry.
19. The method of claim 16 wherein the alteration of wild-type MCC protein is detected by assaying for binding interac¬ tions between said MCC protein and a second cellular protein.
20. The method of claim 19 wherein the second cellular protein is a G protein.
21. The method of claim 16 wherein the alteration of wild-type MCC protein is detected by assaying for phospholipid metabolites.
22. A method of supplying wild-type MCC gene function to a cell which has lost said gene function by virtue of a mutation in an MCC gene, comprising: introducing a wild-type MCC gene into a cell which has lost said gene function such that said wild-type MCC gene is expressed in the cell.
23. The method of claim 22 wherein the wild-type MCC gene introduced recombines with the endogenous mutant MCC gene present in the cell by a double recombination event to correct the MCC gene mutation.
24. A method of supplying wild-type MCC gene function to a cell which has altered MCC said gene function by virtue of a mutation in an MCC gene, comprising: introducing a portion of a wild-type MCC gene into a cell which has lost said gene function such that said portion is expressed in the cell, said portion encoding a part of the MCC protein which is required for non-neoplastic growth of said cell.
25. A method of supplying wild-type MCC gene function to a cell which has altered MCC gene function by virtue of a mutation in an MCC gene, comprising: introducing into the cell a molecule which mimics the function of wild-type MCC.
26. A pair of single stranded DNA primers for determination of a nudeotide sequence of an MCC gene by polymerase chain reac¬ tion, the sequence of said primers being derived from chromosome 5q band 21, wherein the use of said primers in a polymerase chain reac¬ tion results in synthesis of DNA having a sequence as shown in SEQ ID NO: 1.
27. The primers of claim 26 which have restriction enzyme sites at each 5' end.
28. The pair of primers of claim 26 having sequences corre¬ sponding to MCC introns.
29. A nucleic acid probe complementary to human wild-type MCC gene coding sequences.
30. A nucleic acid probe which hybridizes to an exon selected from the group consisting of: nudeotides (1) 2305-2405; and (2) nudeotides 1679 to 1862 as shown in SEQ ID NO: 1.
31. A kit for detecting alteration of wild-type MCC genes comprising a battery of nucleic acid probes which in the aggregate hybridize to all nudeotides of the MCC gene coding sequences.
32. A method of detecting the presence of a neoplastic tis¬ sue in a human, comprising: detecting in a body sample isolated from a human alter¬ ation of a wild-type MCC gene coding sequence or wild-type MCC expression product, said alteration indicating the presence of a neoplastic tissue in the human.
33. The method of claim 32 wherein said body sample is selected from the group consisting of serum, stool, urine and sputum.
34. A method of detecting genetic predisposition to cancer in a human comprising: detecting alteration of wild- type MCC gene coding sequences or their expression products in a human sample selected from the group consisting of blood and fetal tissue, said alteration indicating predisposition to cancer.
35. The method of claim 34 wherein the expression products are mRNA molecules.
36. The method of claim 35 wherein the alteration of wild-type MCC mRNA is detected by hybridization of mRNA from said tissue to an MCC gene probe.
37. The method of claim 34 wherein alteration of wild-type MCC gene coding sequences is detected by hybridization of an MCC gene coding sequence probe to genomic DNA isolated from said tissue.
38. The method of claim 37 wherein the MCC gene coding sequence probe detects a restriction fragment length polymorphism.
39. The method of claim 34 wherein the alteration of wild-type MCC gene coding sequences is detected by determining the sequence of all or part of an MCC gene in said tissue using a polymerase chain reaction, deviations in the MCC sequence deter¬ mined from the sequence of SEQ ID NO: 1 indicating predisposition to cancer.
40. The method of claim 34 wherein the alteration of wild- type MCC gene coding sequences is detected by identifying a mis¬ match between molecules (1) an MCC gene or MCC mRNA isolated from said tissue and (2) a nucleic acid probe complementary to the human wild-type MCC gene coding sequence, when molecules (1) and (2) are hybridized to each other to form a duplex.
41. The method of claim 37 wherein the MCC gene probe hybridizes to an exon selected from the group consisting of: (1) nudeotides 2305 to 2405; and (2) nudeotides 1679 to 1862.
42. The method of claim 34 wherein the alteration of wild- type MCC gene coding sequences is detected by amplification of MCC gene sequences in said tissue and hybridization of the amplified MCC sequences to nucleic acid probes which comprise MCC gene coding sequences.
43. The method of claim 34 wherein the alteration of wild-type MCC gene coding sequences is detected by molecular clon¬ ing of the MCC genes in said tissue and sequencing all or part of the cloned MCC gene.
44. The method of claim 34 wherein the detection of alter¬ ation of wild-type MCC gene coding sequences comprises screening for a deletion mutation.
45. The method of claim 34 wherein the detection of alter¬ ation of wild-type MCC gene coding sequences comprises screening for a point mutation.
46. The method of claim 34 wherein the detection of alter¬ ation of wild-type MCC gene coding sequences comprises screening for an insertion mutation.
47. The method of claim 34 wherein the expression products are protein molecules.
48. The method of claim 47 wherein the alteration of wild-type MCC protein is detected by immunoblotting.
49. The method of claim 47 wherein the alteration of wild-type MCC protein is detected by immunocytochemistry.
50. The method of claim 47 wherein the alteration of wild-type MCC protein is detected by assaying for binding interac¬ tions between said MCC protein and a second cellular protein.
51. The method of claim 50 wherein the second cellular protein is a G protein.
52. A cDNA molecule comprising the coding sequence of the MCC gene.
53. A preparation of the human MCC protein substantially free of other human proteins, the amino acid sequence of said protein corresponding to that shown in SEQ ID NO: 2.
54. A preparation of antibodies immunoreactive with a human MCC protein and not substantially immunoreactive with other human proteins.
PCT/US1992/000377 1991-03-13 1992-01-16 Gene mutated in colorectal cancer of humans Ceased WO1992016656A1 (en)

Priority Applications (7)

Application Number Priority Date Filing Date Title
DE69231245T DE69231245T2 (en) 1991-03-13 1992-01-16 CHANGED GENES IN HUMAN COLOREECTAL CANCER
AU13302/92A AU664834B2 (en) 1991-03-13 1992-01-16 Gene mutated in colorectal cancer of humans
JP50475792A JP3501802B2 (en) 1991-03-13 1992-01-16 Genes mutated in human colorectal cancer
AT92905276T ATE194660T1 (en) 1991-03-13 1992-01-16 ALTERED GENE IN HUMAN COLORECTAL CANCER
DK92905276T DK0580596T3 (en) 1991-03-13 1992-01-16 Gene mutated in colorectal cancer in humans
EP92905276A EP0580596B1 (en) 1991-03-13 1992-01-16 Gene mutated in colorectal cancer of humans
GR20000402138T GR3034446T3 (en) 1991-03-13 2000-09-20 Gene mutated in colorectal cancer of humans.

Applications Claiming Priority (2)

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US07/670,611 US5330892A (en) 1991-03-13 1991-03-13 MCC gene (mutated in colorectal cancer) used for diagnosis of cancer in humans
US670,611 1991-03-13

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EP (1) EP0580596B1 (en)
JP (1) JP3501802B2 (en)
AT (1) ATE194660T1 (en)
AU (1) AU664834B2 (en)
CA (1) CA2105876A1 (en)
DE (1) DE69231245T2 (en)
DK (1) DK0580596T3 (en)
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US5879656A (en) * 1993-10-26 1999-03-09 Thomas Jefferson University Methods of treating metastatic colorectal cancer with ST receptor binding compounds
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US5891629A (en) * 1995-09-28 1999-04-06 Ambion, Inc. Compositions for improving RNase cleavage of base pair mismatches in double-stranded nucleic acids
US5670325A (en) * 1996-08-14 1997-09-23 Exact Laboratories, Inc. Method for the detection of clonal populations of transformed cells in a genomically heterogeneous cellular sample
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