AU4888799A - Mucins - Google Patents

Description

WO 00/04142 PCT/AU99/00579 1 TITLE "MUCINS" FIELD OF THE INVENTION THIS INVENTION relates generally to nucleic acids 5 corresponding to mammalian Mucin genes, and to polypeptides encoded thereby. More particularly, the present invention provides isolated nucleic acids which correspond to Mucin regulatory genes that are predominantly expressed in the colon. These Mucin genes are associated with disease conditions including colorectal cancer, breast cancer, cystic fibrosis, 10 respiratory diseases, inflammatory bowel disease, ulcerative colitis and Crohn's disease and/or any other conditions associated with aberrant Mucin expression, altered properties of mucus or epithelial inflammatory processes involving Mucins. In particular, the present invention provides methods for the diagnosis and therapy of the abovementioned disease conditions. 15 BACKGROUND OF THE INVENTION The increasing sophistication of recombinant DNA technology is greatly facilitating research and development in the medical and allied health fields. This is particularly the case in cancer research. However, despite the effectiveness of this powerful technology, progress has been 20 slow in developing effective recombinant DNA-derived therapeutic or diagnostic agents for cancers. One difficulty has been a lack of understanding of many cancers and other disease conditions. Regulatory genes are an important component of these complex regulatory mechanisms. 25 Cancer suppressor genes, for example, are regulators of cell growth and differentiation (Weinberg et al., 1995, Ann. NY Acad. Sci. 758 331). The paradigm for their role in cancer is that they are trans-acting and recessive at the cellular level; loss of one homologue has no effect on cell function and homozygous inactivation is required for carcinogenesis 30 (Cavenee et al., 1983, Nature 305 779). Colorectal cancers contribute to a major proportion of the WO 00/04142 PCT/AU99/00579 . 2 mortality and morbidity associated with cancer development. There is a particular need, therefore, to understand the complex regulatory mechanisms associated with colorectal cancers as well as cancers in anatomically adjacent regions. 5 The epithelial mucins are a family of secreted and cell surface glycoproteins expressed by epithelial tissues. They are characterised by a central polymorphic tandem repeat structure, which comprises most of the protein backbone, and a large number of O-linked carbohydrate side chains (Gum et al., 1995, Biochem. Soc. Trans. 23 795). The complex structure and 10 large size of these molecules makes it difficult to characterise them using classical biochemical techniques. The genes are also difficult to clone because of their large size and the presence of GC-rich tandem repeats. Ten mucin genes have been identified; MUC3, MUC4, MUC5AC, MUC5B, MUC6 and MUC8 have been partially cloned and full-length cDNA clones 15 are available for MUC1, MUC2, MUC7 and MUC9. Mucins are known to contribute to pathology in a number of epithelial diseases including cystic fibrosis (CF), inflammatory bowel disease (IBD) and adenocarcinomas. Gastrointestinal mucins which have been described to date include: the transmembrane mucins MUC1 and MUC4; the 20 gel-forming mucins MUC2, MUC5AC and MUC6; and MUC3 which has an unclear structure and function. As used herein, Mucin genes or isolated nucleic acids corresponding thereto will be expressed in italicized form as MUC. Mucin polypeptides will be expressed as MUC. 25 Immunohistochemical staining and Western blotting analysis with mature MUC1-specific antibodies revealed that MUC1 became ectopically expressed in colorectal tumours and levels were significantly higher in primary tumours of patients with metastases. Experimentally increased expression of gel-forming mucins resulted in increased metastasis 30 in colon cancer cells in xenograft metastasis models (Ho et al., 1995, Int. J. Oncol. 7 913). Northern blot analysis has been employed to investigate WO 00/04142 PCT/AU99/00579 3 expression of MUCI, MUC2, MUC3 and MUC4 in paired normal and colonic tumour tissues and in nine colorectal cancer (CRC) cell lines (Ogata et al., 1992, Cancer Res. 52 5971). MUCI and MUC4 were present in colonic mucosa with similar expression levels in carcinomas, but occasionally 5 elevated levels of MUC4 were apparent. Levels of MUC2 and MUC3 were decreased by varying degrees in the tumours of most patients. There was no apparent correlation between the expression of any mucin gene and the site, stage or histological type of tumour. All four mucin genes were expressed at low levels or not at all in the nine CRC cell lines under 10 investigation; MUCI transcripts were detected in COL0205, MUC2 and MUC4 probes hybridised weakly to all nine cell lines, and MUC3 expression was observed in five of the lines. Using a combination of in situ hybridisation and immunohistochemistry, Chang et al (Chang et al., 1994, Gastroenterology 107 28) also found MUC2 and MUC3 were downregulated 15 in CRC. A more recent in situ hybridisation study found expression of MUC2 and MUC3 mRNA was markedly reduced in poorly, moderately and well differentiated colorectal tumours but preserved in mucinous carcinomas (Weiss et al., 1996, J. Histochem. Cytochem. 44 1161). It is noted that MUC3 is located on human chromosome 7q22, or an equivalent location on 20 other mammalian chromosomes, and is primarily expressed under normal conditions in the small intestine (Shekels et al., 1998, Biochem J. 330 1301). OBJECT OF THE INVENTION The present inventors have realized that the Mucins constitute an incomplete family of genes and gene products implicated in a variety of 25 disease conditions. Surprisingly, the present inventors have identified novel Mucin genes located on human chromosome 7q22, and isolated novel nucleic acids corresponding thereto. Furthermore, the present inventors have found that these novel Mucin genes are predominantly expressed in the colon, and may be involved in cancer of the large bowel, cystic fibrosis, 30 breast cancer, inflammatory bowel disease, ulcerative colitis respiratory diseases and Crohn's disease and/or any other conditions associated with WO 00/04142 PCT/AU99/00579 4 aberrant Mucin expression, altered properties of mucus or epithelial inflammatory processes involving Mucins. It is therefore an object of the invention to provide novel Mucin genes and isolated nucleic acids corresponding thereto. 5 SUMMARY OF THE INVENTION The present invention is broadly directed to an isolated MUC nucleic acid which corresponds to a MUC gene located on mammalian chromosome 7q22, or on a mammalian chromosome structurally or functionally equivalent thereto, which MUC gene is normally predominantly 10 expressed in the colon. In a first aspect, the MUC gene of the present invention is MUC 11. Accordingly, "a MUC11 nucleic acid" means an isolated nucleic acid of the invention which corresponds to the MUCI I gene. Preferably, the isolated MUC11 nucleic acid comprises a 15 nucleotide sequence encoding an amino acid sequence which comprises SGLSEESTTSHSSPGSTHTTLSPASTTT (SEQ ID NO: 1). More preferably, the isolated MUC1 I nucleic acid comprises a nucleotide sequence encoding the amino acid sequence according to SEQ ID NO:3. 20 Even more preferably, the isolated MUC11 nucleic acid comprises a nucleotide sequence according to SEQ ID NO: 2. In a second aspect, the MUC gene of the present invention is MUC12. Accordingly, "a MUC12 nucleic acid" means an isolated nucleic acid of the invention which corresponds to the MUC12 gene. 25 Preferably, the isolated MUC12 nucleic acid comprises a nucleotide sequence encoding an amino acid sequence which comprises SGLSQESTTFHSSPGSTETTLAPASTTT (SEQ ID NO: 4). More preferably, the isolated MUC12 nucleic acid comprises a nucleotide sequence encoding the amino acid sequence according to SEQ 30 ID NO:6. Even more preferably, the isolated MUC12 nucleic acid WO 00/04142 PCT/AU99/00579 5 comprises a nucleotide sequence according to SEQ ID NO: 5. In a third aspect, the present invention resides in an isolated MUC polypeptide. In one embodiment, the isolated MUC polypeptide has an 5 amino acid sequence according to SEQ ID NO: 3, hereinafter referred to as a "MUCI 1 polypeptide". In another embodiment, the isolated MUC polypeptide has an amino acid sequence according to SEQ ID NO:6, hereinafter referred to as a "MUC12 polypeptide". 10 In a fourth aspect, the present invention resides in an antibody specific for a MUC polypeptide (hereinafter referred to as an anti-MUC antibody). Preferably, the anti-MUC antibody is selected from the group consisting of: 15 (i) an anti-MUC1 1 IgM monoclonal antibody hereinafter referred to as M1 1.9; and (ii) an anti-MUC12 IgM monoclonal antibody hereinafter referred to as M12.15. In a fifth aspect, the present invention resides in methods of 20 detecting a MUC gene, a MUC gene transcript or a MUC polypeptide. The fifth aspect extends to methods for detecting a polymorphism, deletion, mutation, truncation or expansion in a MUC gene, a MUC gene transcript or a MUC polypeptide, or detecting a level of expression thereof. One embodiment of the fifth aspect is directed to use of an isolated MUC nucleic 25 acid to determine whether a mammal has a disease condition, or a predisposition thereto. Another embodiment is directed to use of an isolated MUC polypeptide to determine whether a mammal has a disease condition, or a predisposition thereto. In a sixth aspect, the present invention provides a method of 30 gene therapy of a disease condition in a mammal, said method including administering to said mammal a gene therapy construct which includes an WO 00/04142 PCT/AU99/00579 6 isolated MUC nucleic acid as hereinbefore defined, to thereby alleviate one or more symptoms of said disease condition in said mammal. In a seventh aspect, the present invention provides a method of treating a disease condition in a mammal, said method comprising the 5 step of administering to said mammal a pharmaceutically effective amount of a MUC polypeptide or an anti-MUC antibody. In an eigth aspect, the present invention resides in a pharmaceutical composition comprising a MUC polypeptide or anti-MUC antibody, together with a pharmaceutically acceptable carrier and/or diluent. 10 Preferably, the mammal is a human. As used herein, the "disease condition" is associated with aberrant Mucin expression, altered properties of mucus or epithelial inflammatory processes involving Mucins. Preferably, the disease condition is selected from the group 15 consisting of colorectal cancer (CRC), cystic fibrosis (CF), inflammatory bowel disease (IBD), breast cancer (BC), Crohn's disease, ulcerative colitis, asthma and chronic bronchitis. More preferably, the disease condition is selected from the group consisting of colorectal cancer (CRC), cystic fibrosis (CF), 20 inflammatory bowel disease (IBD) and breast cancer (BC). As used herein, unless the context requires otherwise, the word "comprise", or variations such as "comprises" or "comprising", will be understood to imply the inclusion of a stated element or integer or group of elements or integers but not the exclusion of any other element or integer or 25 group of elements or integers. BRIEF DESCRIPTION OF THE DRAWINGS FIG. 1(A): Autoradiograph of a differential display gel showing amplified products from RNA isolated from matched normal colon (N) and primary colorectal tumor (P) tissues. Differentially 30 expressed bands dd29 (MUC12) and dd34 (MUC11) are arrowed.

WO 00/04142 PCT/AU99/00579 7 FIG. 1(B): Northern blot analysis of total RNA from patient 101 hybridized with the dd29 probe to detect a MUC12 gene transcript (mRNA). Signal corresponding to 18S ribosomal RNA is shown as a loading control. 5 FIG. 1(C): Northern blot analysis of RNA from patient 112 hybridized with the dd34 probe to detect a MUCI I gene transcript (mRNA) . Signal corresponding to 18S ribosomal RNA is shown as a loading control. FIG. 1(D): Multiplex semi-quantitative RT-PCR showing amplification of 10 MUC12 mRNA transcripts from matched normal colonic mucosa and primary tumor # 40, normal mucosa from patient # 81 and six colorectal cancer cell lines. Amplification of P 2 microglobulin (-MG) is included as a measure of total RNA. FIG. 1(E): Multiplex semi-quantitative RT-PCR showing amplification of 15 MUCI I mRNA transcripts in matched normal colonic mucosa and primary tumors of patients # 40, 164, and 97 and six colorectal cancer cell lines. Amplification of 2 -microglobulin (p-MG) is included as a measure of total RNA. FIG. 1(F): Multiplex semi-quantitative RT-PCR showing amplification of 20 MUC12 mRNA transcripts from matched normal colonic mucosa and primary tumors # 346, 84, 128, 97 and 316 and from five unpaired Dukes' stage D tumors (M) # 93, 361, 107, 357 and 367. Amplification of P 2 -microglobulin (P -M/lG) is included as a measure of total RNA. 25 FIG. 1(G): Multiplex semi-quantitative RT-PCR showing MUC11 mRNA transcripts in matched normal colonic mucosa and primary tumors of patients # 110, 346, 84, 128, and 348 and from five unpaired Dukes' stage D tumors (M) # 93, 107, 361, 367 and 357. Amplification of P 2 -microglobulin

(

2 -MG) is included as 30 a measure of total RNA. Ma denotes molecular size markers in FIG 1D-G.

WO 00/04142 PCT/AU99/00579 . 8 FIG. 2: Predicted amino acid sequence of MUC12. Numbering of amino acids is given on the right. The consensus sequence of the degenerate tandem repeat structure is shown at the top. The two cysteine-rich EGF-like domains are double 5 underlined, a potential coiled-coil domain is in bold, the hydrophobic domain singly underlined and potential N glycosylation sites shaded. The stop codon is denoted by an asterisk. FIG. 3: Amino acid sequence alignment of the carboxyl termini of 10 MUC12, hMUC3 (amino acids 1-366), mMuc3 (Shekels et al., 1998, supra; amino acids 637-1015), rMuc3 (Gum et al., 1991, supra; Khatri et al., 1997, Biochem. Biophys. Acta 1326 7; amino acids 356-447 and 1-379 respectively), hMUC4 (Moniaux et al., 1998, Biochem. J. 338 1998; amino acids 861 15 1156) and rMuc4 (Sheng et al., 1992, J. Biol. Chem. 267 16341; amino acids 451-744). Light shading demonstrates identity with MUC12 and dark shading highlights all cysteine residues. Hyphens indicate gaps inserted to optimize the alignment. 20 FIG. 4: Predicted amino acid sequence of MUC11 showing the degenerate tandem repeat structure. The consensus sequence is shown at the top and amino acids not consistent with this sequence are shown in bold. Hyphens indicate gaps placed in order to optimize the amino acid alignment. A 25 potential N-glycosylation site is shaded. FIG. 5: mRNA tissue distribution of the 7q22 mucin gene family. Only those tissues showing a positive signal by Northern blot analysis are represented in the histogram. Sixteen tissues of neural origin, heart, aorta, skeletal muscle, bladder, stomach, 30 testis, ovary, spleen, pituitary gland, adrenal gland, thyroid gland, salivary gland and mammary gland were negative for WO 00/04142 PCT/AU99/00579 . 9 mucin mRNA expression. Expression was quantified by densitometry and is shown as a proportion of the tissue showing highest expression. FIG. 6: Domain organization of the C-termini of human MUC12, 5 hMUC3, the rodent Muc3 mucins and the rat and human MUC4 mucins. The relative size of domains is accurate except that the N-glycosylated domain adjacent to the mucin domain in MUC4 is shown at approximately one fifth of its actual size. Only the beginning of the large mucin domains are shown. 10 FIG. 7: Alignment of the first extracellular EGF-like domain of MUC12 with human EGF-like growth factors. Dark shading highlights identical amino acids and light shading indicates conservative amino acid substitutions. FIG. 8: Schematic representation of MUC 11 cloning (A) and MUC 12 15 cloning (B). FIG. 9: Normal colonic expression patterns of MUCI 1 (A, B) and MUC12 (C) polypeptides as determined by anti-MUC mAb M11.9 and M12.15 immunostaining, respectively. (D) shows MUC 11 gene transcript (mRNA) expression detected by in situ 20 hybridization in normal colonic epithelium and loss of expression in CRC (top right). FIG. 10: Expression of MUC11 and MUC12 mRNA in normal colon as detected by RT-PCR. Cytokeratin 20, (CK20) a colonic epithelial marker, was employed as a loading control. 'RC' 25 denotes right colon, 'TC' the transverse colon, 'LC' the left colon, 'SC' sigmoid colon; 'CA' refers to the caecum and 'R' denotes the rectum. FIG. 11: Expression of MUC11 and MUC12 mRNA in CRC cell lines as detected by RT-PCR. The loading control is p 2 -microglobulin 30 (B2MG) and 'M' denotes the molecular weight marker. FIG. 12: Expression of MUC11 and MUC12 mRNA in IBD as detected WO 00/04142 PCT/AU99/00579 10 by RT-PCR. Cytokeratin 20 (CK20) a colonic epithelial marker, was employed as a loading control. 'N' denotes tissues which appear macroscopically normal and 'D' refers to tissues reported to have IBD. 'CA' refers to the caecum, 'CO' the colon, 5 'LC' the left colon, 'TC' the transverse colon, 'RS' the recto sigmoid colon, 'Sl' the small intestine, 'IL'denotes the ileum and 'IP' an ileal pouch. FIG. 13: Expression of MUC11 and MUC12 mRNA in BC as detected by RT-PCR. The loading control is P 2 microglobulin denoted by 10 B2MG and the molecular weight marker is denoted by 'M'. The positive control was normal colonic cDNA from patient 164. FIG 14: Northern blot analysis of MUC11 expression in normal colon (N) and primary CRC (P) of six patients, assessed using a probe corresponding to dd34. The position of ribosomal RNAs 15 are indicated, and signal from 18S ribosomal RNA was used as a loading control. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS The present invention is predicated in part on the identification of novel MUC11 and MUC12 genes which are normally predominantly 20 expressed in the colon. The isolated MUC nucleic acids and MUC genes of the invention may be useful in treatment and diagnosis of disease conditions associated with aberrant Mucin expression, altered properties of mucus or epithelial inflammatory processes involving Mucins. Such disease conditions include but are not limited to cancer of the large bowel (CRC), cystic fibrosis 25 (CF), inflammatory bowel disease (IBD), respiratory diseases such as asthma and chronic bronchitis, breast cancer (BC), ulcerative colitis and Crohn's disease. The present invention is particularly directed to cancers of the large bowel, which includes the colon, rectum and anal canal, such as CRC, 30 although it extends to biochemically, physiologically and/or genetically related cancers in other parts of the gastrointestinal tract.

WO 00/04142 PCT/AU99/00579 11 The MUC genes are, for example, down-regulated in CRC. By "predominantly expressed" is meant that a MUC gene transcript or MUC polypeptide encoded by said MUC gene is expressed in the colon at a level greater than in any other organ. 5 By "associated with" is meant that the disease condition displays symptoms consistent with aberrant Mucin expression, altered properties of mucus or epithelial inflammation involving Mucins. The disease association may be merely correlative or may reflect a causative role of Mucins in the disease condition. 10 The term "cancer" is used in its broadest sense to include malignant tumours, carcinomas and sarcomas. In light of the foregoing, it will be appreciated that a MUC nucleic acid "corresponds to" a MUC gene by being an isolated nucleic acid derived from said MUC gene, or a portion thereof. Thus it will be understood 15 that said gene has components including amino acid coding sequences and non-coding sequences. Non-coding sequences include, for example, introns and regulatory sequences which include a promoter, translation initiation and termination sequences and a polyadenylation sequence, for example. The isolated MUC nucleic acid may therefore correspond to some or all of the 20 aforementioned components of the corresponding MUC gene. It should be noted that MUC terminology has recently undergone revision. In particular, MUC12 was formerly known as dd 29 or MUC10. Also, MUCI 1 was formerly known as dd 34. Therefore, with this in mind, should the term "MUC10" or "dd29" be encountered herein, it should 25 in all cases be taken to mean MUC12. It will also be understood that a MUC polypeptide is encoded by an isolated MUC nucleic acid or by a MUC gene as hereinbefore defined. Isolated MUC nucleic acids of the invention may be in DNA (e.g. cDNA or genomic DNA), RNA (e.g. mRNA) or hybrid DNA:RNA form, 30 eithre in double-stranded or single-stranded form. For example, single stranded MUC nucleic acids include nucleic acids having sequences WO 00/04142 PCT/AU99/00579 12 complementary to the nucleotide sequences of SEQ ID NO:2 and SEQ ID NO:5. In one embodiment, the isolated MUC nucleic acid of the invention comprises a nucleotide sequence having at least 60% identity to 5 the nucleotide sequence according to SEQ ID NO:2, or a nucleotide sequence capable of hybridizing thereto under at least low stringency conditions. In another embodiment, the isolated MUC nucleic acid of the invention comprises a nucleotide sequence having at least 60% identity to 10 the nucleotide sequence according to SEQ ID NO:5, or a nucleotide sequence capable of hybridizing thereto under at least low stringency conditions. According to these embodiments, it is preferable that the nucleotide sequence has at least 75% identity. 15 More preferably, the nucleotide sequence has at least 90% sequence identity. The term "identity" is used herein in its broadest sense to include the number of exact nucleotide or amino acid matches having regard to an appropriate alignment using a standard algorithm, such as but not 20 limited to the Geneworks program (Intelligenetics). For this purpose, BLAST family programs may also be useful (Altschul et al., 1997, Nucl. Acids Res. 25 3389, which is herein incorporated by reference). A detailed discussion of sequence analysis can be found in Unit 19.3 of CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Eds Ausubel et al., (John Wiley & Sons), which 25 is herein incorporated by reference. According to these embodiments, it is preferable that the nucleotide sequence is capable of hybridizing under medium stringency conditions. More preferably, the nucleotide sequence is capable of 30 hybridizing under high stringency conditions Reference herein to low stringency conditions includes and WO 00/04142 PCT/AU99/00579 _ 13 encompasses from at least about 1 % v/v to at least about 15% v/v formamide and from at least about 1 M to at least about 2 M salt for hybridisation at 420C, and at least about 1 M to at least about 2 M salt for washing at 420C. Low stringency conditions also include 1 % Bovine Serum 5 Albumin (BSA), 1 mM EDTA, 0.5 M NaHPO 4 (pH 7.2), 7% SDS for hybridization at 650C, and (i) 2xSSC, 0.1% SDS; or (ii) 0.5% BSA, 1 mM EDTA, 40 mM NaHPO 4 (pH 7.2), 5% SDS for washing at room temperature. Medium stringency conditions include and encompass from at least about 16% v/v to at least about 30% v/v formamide and from at least 10 about 0.5 M to at least about 0.9 M salt for hybridisation at 42 0 C, and at least about 0.5 M to at least about 0.9 M salt for washing at 420C. Medium stringency conditions also include 1 % Bovine Serum Albumin (BSA), 1 mM EDTA, 0.5 M NaHPO 4 (pH 7.2), 7% SDS for hybridization at 65*C, and (i) 2 x SSC, 0.1% SDS; or (ii) 0.5% BSA, 1 mM 15 EDTA, 40 mM NaHPO 4 (pH 7.2), 5% SDS for washing at 42TC. High stringency includes and encompasses from at least about 31 % v/v to at least about 50% v/v formamide and from at least about 0.01 M to at least about 0.15 M salt for hybridisation at 42*C, and at least about 0.01 M to at least about 0.15 M salt for washing at 420C. 20 High stringency also includes 1% BSA, 1 mM EDTA, 0.5 M NaHPO 4 (pH 7.2), 7% SDS for hybridization at 650C, and (i) 0.2 x SSC, 0.1 % SDS; or (ii) 0.5% BSA, 1mM EDTA, 40 mM NaHPO 4 (pH 7.2), 1% SDS for washing at a temperature in excess of 650C. In general, washing is carried out at Tm = 69.3 + 0.41 (G + C) 25 % = -120C. However, the Tm of a duplex DNA decreases by 100 with every increase of 1% in the number of mismatched based pairs. Although the MUC genes and isolated MUC nucleic acids of the present invention are exemplified in relation to the human mammalian species, the present invention extends to orthologs in non-human mammals 30 such as in primates, laboratory test animals (e.g. mice, rates, rabbits, guinea pigs, hamsters), companion animals (e.g. dogs, cats), livestock animals (e.g.

WO 00/04142 PCT/AU99/00579 14 sheep, pigs, horses, donkeys, cows) and captive wild animals (e.g. deer, fox). In light of the foregoing, the term "MUC homologs" is used to encompass MUC orthologs, isolated nucleic acids which hybridize to MUC nucleic acids of the invention and isolated nucleic acids which display at 5 least 60% sequence identity to isolated MUC nucleic acids. It will also be appreciated that MUC homologs encompass single or multiple nucleotide substitutions, deletions and/or additions to the isolated MUC nucleic acids of the invention, inclusive of mutants, fragments, parts, portions and segments of the nucleotide sequences of the invention. 10 The isolated MUC nucleic acids of the present invention and homologs thereof therefore include oligonucleotides, primers (such as for PCR), antisense sequences, molecules suitable for use in co-suppression and fusion nucleic acid molecules. Ribozymes are also contemplated by the present invention. It will be understood that probes, primers and antisense 15 sequences correspond to distinct portions of isolated MUC nucleic acids of the invention, in that they contain nucleotide sequences based on said distinct portions of an isolated MUC nucleic acid sequence. Such probe and primer sequences may be based on a MUC sequence of the invention by being identical thereto, or by being degenerate with respect thereto. 20 As used herein, "oligonucleotides" are nucleic acids which comprise a contiguous sequence of no more than seventy (70) nucleotides, whereas "polynucleotides" are nucleic acids which comprise a contiguous sequence of more than seventy (70) nucleotides. A "probe" may be an oligonucleotide or a polynucleotide, either double-stranded or single 25 stranded, for use in hybridization techniques such as Northern blotting, Southern blotting or in situ hybridization. The skilled person will realize that in situ hybridization also includes Fluorescence In Situ Hybridization (FISH), which is used for determining chromosomal localization. In situ hybridization techniques applicable to the present invention will be described in detail 30 hereinafter. A "primer" is a nucleic acid (usually an oligonucleotide) capable WO 00/04142 PCT/AU99/00579 15 of annealing to a nucleic acid template under appropriate conditions of ionic strength and temperature, which annealed primer can be extended in a template-dependent fashion by a suitable nucleic acid polymerase (for example Taq polymerase or Sequenase T M ). It will therefore be understood 5 that primers of the invention may be useful for PCR, sequencing, RACE, primer extension and the like. In use, isolated MUC nucleic acids, probes and primers may be modified such as by end-labeling with 3 1P-ATP and T4 polynucleotide kinase or by random primed labeling with 32 P-dCTP and DNA polymerase. 10 Biotinylation is also contemplated, as is modification with phosphorothiorates, fluorochromes, digoxigenin, enzymes and peptides, for example. It is contemplated that diagnostic methods may be employed which utilize isolated MUC nucleic acids of the present invention, or portions thereof such as probes and PCR primers. Also, diagnostic methods 15 employing MUC polypeptides will be discussed in more detail hereinafter. Diagnostic methods may include detection of MUC genes, transcripts and/or polypeptides in samples such as fecal specimens and/or in colonic biopsies, analysis of serum MUC levels in patients with epithelial diseases including cancers, breast tissue biopsy samples or in respiratory 20 mucus samples from patients suffering from CF, asthma or chronic bronchitis. The diagnostic methods of the present invention may therefore be applicable to determining whether an individual has a disease condition associated with aberrant Mucin expression, altered properties of mucus or epithelial inflammatory processes involving Mucins, or a predisposition to 25 said disease. It will be appreciated that "predisposition" as used herein refers to an increased probability that an individual will contract the disease. However, it will also be appreciated that the diagnostic methods may also indicate whether an individual actually suffers from the disease, assist in assessing the severity of disease, a prognosis of the likely course of disease 30 and appropriate treatments for the disease. Thus, the diagnostic methods of the invention may be useful whether or not the individual suffers from one or WO 00/04142 PCT/AU99/00579 16 more symptoms of the disease. The present invention therefore contemplates methods of detecting MUC genes and MUC gene transcripts (e.g. mRNA), such as involving hybridization techniques (for example, by Northern or Southern 5 blotting or in situ hybridization) or polynucleotide sequence amplification techniques (for example RT-PCR). Such methods may detect: (i) a polymorphism, deletion, mutation, expansion, and/or truncation in a MUC gene or MUC gene transcript; and (ii) a relative level of expression of a MUC gene transcript 10 (an mRNA transcript derived from a MUC gene). Such methods of detection facilitate determination of whether said MUC gene is aberrantly-expressed as an indication of a disease condition or a predisposition thereto. Also, MUC gene polymorphisms, deletions, mutations, truncations or deletions may be detected which indicate 15 a disease condition or a predisposition thereto. It will be appreciated, for example, that measurement of a relative level of expression of a MUC gene transcript facilitates diagnostic assessment of whether MUC gene expression is downregulated and thereby indicative of CRC. 20 Although PCR is the preferred nucleic acid sequence amplification technique, It will be appreciated that there are a variety of polynucleotide sequence amplification techniques other than PCR, which include rolling circle amplification (RCA) and strand displacement amplification (SDA). With regard to RCA, reference is made to W097/19193 25 which is herein incorporated by reference. With regard to SDA, reference is made to U.S. Patent No. 5455166, which is herein incorporated by reference. Detailed PCR methods are provided hereinafter, although the skilled person is also referred to Chapter 15 of CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Eds Ausubel et al., (John Wiley & Sons), which is 30 herein incorporated by reference, for a detailed discussion and examples of PCR methods.

WO 00/04142 PCT/AU99/00579 17 It will also be understood that PCR includes within its scope RT-PCR and multiplex PCR as will be described in detail hereinafter. Such methods may be used for qualitative or semi-quantitative analysis. PCR based Restriction Fragment Length Polymorphism (PCR-RFLP) methods are 5 also contemplated, which methods are useful when a polymorphism, deletion mutation, truncation and/or expansion either introduces or removes one or more restriction endonuclease sites in a MUC gene. The skilled person will appreciate that Northern, Southern and in situ hybridization methods involve formation of a hybrid nucleic acid 10 comprising a MUC gene or mRNA transcript and a corresponding isolated MUC nucleic acid or portion thereof. RNA isolation and Northern hybridization methods are described in detail herein, although the skilled person is also referred to Chapter 4 of CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Eds 15 Ausubel et al., (John Wiley & Sons), which is herein incorporated by reference. Furthermore, Southern hybridization methods are described in detail herein, although the skilled person is also referred to sections 2.9A-B and 2.10 of CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Eds 20 Ausubel et al., (John Wiley & Sons), which is herein incorporated by reference. Also, determining whether a MUC gene or MUC gene transcript includes a polymorphism, mutation, deletion, truncation and/or expansion can be performed using methods such as PCR-RFLP analysis, Single Strand 25 Conformational Polymorhpism (SSCP) analysis and Denaturing Gradient Gel Electrophoresis (DGGE). These techniques have become well known in the art of mutation detection. A non-limiting example of DGGE is provided in Folde & Loskoot, 1994, Hum. Mut. 3 83, which is herein incorporated by reference. A non-limiting example of specific allele detection by PCR-RFLP 30 and SSCP is provided in Lappalainen et al., 1995, Genomics 27 274, which is herein incorporated by reference.

WO 00/04142 PCT/AU99/00579 . 18 It is proposed that mutations in MUCI I or MUC12 genes are associated with bowel cancers (CRC), CF, BC, IBD, chronic bronchitis, asthma, ulcerative colitis and/or Crohn's disease. These are examples of disease conditions associated with aberrant Mucin expression, altered 5 properties of mucus or epithelial inflammatory processes involving Mucins. The isolated MUC nucleic acids now provide a means for genetic screening of the abovementioned disease conditions in human and other mammalian species. Genetic screening may be conducted by determining full expression or full-length transcript production by Northern blot, cloning and sequencing 10 of the MUC genes or identifying mutations by oligonucleotide hybridisation or by direct sequencing of PCR amplification products of the MUC genes. In addition, the present invention extends to nucleic acid molecules having translation-terminating mutations leading to truncation mutants. The detection of truncation mutants may be important for genetic analysis of people with, 15 for example, cancer of the large bowel or with a propensity to develop large bowel cancer, determined on, for example, hereditary grounds. Truncated MUC polypeptides may also be useful in developing therapeutic agents such as antagonists or for developing antibodies. Truncational mutants may be readily detected by a direct protein truncation 20 test. In essence, DNA fragments including PCR amplification products or corresponding mRNA molecules are subjected to in vitro translation and optionally also transcription and the translation products assayed by, for example, SDS-PAGE or by differential antibody binding assays. This assay may also be employed to screen for agents capable of inducing truncation 25 mutations or for agents acting as antagonists for truncation mutant-inducing agents. Alternatively, MUC polypetides may be assayed by, for example, by antibody screening such as in an ELISA. Thus, it will be appreciated that the present invention 30 contemplates isolated MUC polypeptides, and also: (i) polypeptides which comprise an amino acid sequence WO 00/04142 PCT/AU99/00579 19 having at least 60% identity to a MUC polypeptide amino acid sequence, preferably at least 75% identity thereto, or more preferably at least 90% identity thereto; and 5 (ii) polypeptides encoded by MUC homologs. Such polypeptides are hereinafter referred to as "MUC homologs". The MUC polypeptide homologs of the invention include amino acid substitution(s), deletion(s) and/or addition(s) to a MUC polypeptide 10 sequence. Particular examples include antigenic fragments and analogues useful in immunoassays and as therapeutic agents as well as other fragments carrying B cell and/or T cell linear or conformational epitopes. Additions to the amino acid sequence include fusion partners in the form of peptides or polypeptides, which create a MUC fusion polypeptide. 15 Fusion polypeptides include the MUC polypeptide(s) together with fusion partners such as HIS 6 , glutathione-s-transferase (GST), thioredoxin (TR) and maltose binding protein (MBP). Fusion partners greatly assist recombinant synthetic polypeptide purification by virtue of each fusion partner affording affinity purification by a specific affinity matrix. Preferably, 20 the fusion polypeptide also includes a protease-specific cleavage site, so that the fusion partner may be cleaved and removed following purification to leave a substantially unmodified MUC polypeptide. The use of fusion partners for purification of recombinant expressed polypeptides is well known in the art. Indeed, there are a variety 25 of commercial sources applicable to fusion partners and purification systems such as the QlAexpressTM

(HIS)

6 system, the Pharmacia GST purification system and the New England Biolabs MBP system. Also within the scope of fusion partners are "epitope tags". Such tags are well known in the art and include c-myc, influenza 30 hemagglutinin and FLAG tags. Furthermore, Green Fluorescent Protein (GFP) is a well known WO 00/04142 PCT/AU99/00579 20 fusion partner applicable to MUC polypeptides of the invention. A particularly useful application of GFP fusion partners is in the visible identification of cells or tissues which express a GFP-MUC fusion polypeptide of the invention. Identification may be performed by flow cytometry or fluorescence 5 microscopy, as are well known in the art. The MUC polypeptides and MUC homologs of the invention may be in recombinant form of may be chemically synthesized, as is well known in the art. Chemical synthesis is preferably suited to production of MUC peptides. As used herein, "peptides" have no more than fifty (50) 10 contiguous amino acids. Preferably, MUC polypeptides are in recombinant form. In order to produce recombinant MUC polypeptides, isolated MUC nucleic acids of the present invention may be ligated into an expression vector to form an expression construct capable of directing expression of said 15 MUC nucleic acid in a prokaryotic cell (for example, E. coli) or in a eukaryotic cell (for example, yeast cells, fungal cells, insect cells, mammalian cells or plant cells). Suitably, the expression vector comprises one or more regulatory elements which direct expression of the nucleic acid ligated in said 20 expression construct. Such regulatory sequences include promoters, enhancers, splice donor/acceptor sites, polyadenylation sequences, translation initiation (Kozak sequences) and translation termination signals. Suitable promoters may be constitutive (for example, CMV- or SV40-derived promoters) or inducible (for example, Zn responsive metallothionein 25 promoters) or repressible (tet-repressible promoters). Exemplary methods useful for recombinant protein expression and purification, including fusion polypeptides, can be found in Chapters 16 of CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (Eds. Ausubel et al.; John Wiley & Sons Inc., 1997 Edition) and Chapters 5 and 6 of CURRENT 30 PROTOCOLS IN PROTEIN SCIENCE (Eds. Coligan et al.; John Wiley & Sons Inc., 1997 Edition) which are herein incorporated by reference.

WO 00/04142 PCT/AU99/00579 . 21 "Analogues" of the MUC polypeptides of the invention contemplated herein include, but are not limited to, modification to side chains, incorporating of unnatural amino acids and/or their derivatives during peptide, polypeptide or protein synthesis and the use of crosslinkers and 5 other methods which impose conformational constraints on the proteinaceous molecule or their analogues. Such chemical analogues may be useful in providing stable means for diagnostic purposes or for producing agonists or antagonists or for producing stable molecules for use in natural product screening. 10 Examples of side chain modifications contemplated by the present invention include modifications of amino groups such as by reductive alkylation by reaction with an aldehyde followed by reduction with NaBH 4 ; amidination with methylacetimidate; acylation with acetic anhydride; carbamoylation of amino groups with cyanate; trinitrobenzylation of amino 15 groups with 2, 4, 6-trinitrobenzene sulphonic acid (TNBS); acylation of amino groups with succinic anhydride and tetrahydrophthalic anhydride; and pyridoxylation of lysine with pyridoxal-5-phosphate followed by reduction with NaBH 4 . The guanidine group of arginine residues may be modified by 20 the formation of heterocyclic condensation products with reagents such as 2,3-butanedione, phenylglyoxal and glyoxal. The carboxyl group may be modified by carbodiimide activation via 0-acylisourea formation followed by subsequent derivitisation, for example, to a corresponding amide. 25 Sulphydryl groups may be modified by methods such as carboxymethylation with iodoacetic acid or iodoacetamide; performic acid oxidation to cysteic acid; formation of a mixed disulphides with other thiol compounds; reaction with maleimide, maleic anhydride or other substituted maleimide; formation of mercurial derivatives using 4-chloromercuribenzoate, 30 4-chloromercuriphenylsulphonic acid, phenylmercury chloride, 2 chloromercuri-4-nitrophenol and other mercurials; carbamoylation with WO 00/04142 PCT/AU99/00579 22 cyanate at alkaline pH. Tryptophan residues may be modified by, for example, oxidation with N-bromosuccinimide or alkylation of the indole ring with 2 hydroxy-5-nitrobenzyl bromide or sulphenyl halides. Tyrosine residues on 5 the other hand, may be altered by nitration with tetranitromethane to form a 3-nitrotyrosine derivative. Modification of the imidazole ring of a histidine residue may be accomplished by alkylation with iodoacetic acid derivatives or N carbethoxylation with diethylpyrocarbonate. 10 Examples of incorporating unnatural amino acids and derivatives during peptide synthesis include, but are not limited to, use of norleucine, 4-amino butyric acid, 4-amino-3-hydroxy-5-phenylpentanoic acid, 6-aminohexanoic acid, t-butylglycine, norvaline, phenylglycine, ornithine, sarcosine, 4-amino-3-hydroxy-6-methylheptanoic acid, 2-thienyl alanine 15 and/or D-isomers of amino acids. A list of unnatural amino acids, contemplated herein is shown in Table 1. Crosslinkers can be used, for example, to stabilise tertiary conformation, using homo-bifunctional crosslinkers such as the bifunctional imido esters having (CH 2 )n spacer groups with n=1 to n=6, glutaraldehyde, N-hydroxysuccinimide esters and 20 hetero-bifunctional reagents which usually contain an amino-reactive moiety such as N-hydroxysuccinimide and another group specific-reactive moiety such as maleimido or dithio moiety (SH) or carbodiimide (COOH). In addition, peptides can be conformationally constrained by, for example, incorporation of Ca and Na-methylamino acids, introduction of double bonds 25 between Ca and Cp atoms of amino acids and the formation of cyclic peptides or analogues by introducing covalent bonds such as forming an amide bond between the N and C termini, between two side chains or between a side chain and the N or C terminus. The present invention further contemplates chemical analogues 30 of the polypeptides of the invention capable of acting as antagonists or agonists thereof, or which can act as functional analogues thereof. Chemical WO 00/04142 PCT/AU99/00579 23 analogues may not necessarily be derived from the polypeptides of the invention, but may share certain conformational similarities. Alternatively, chemical analogues may be specifically designed to mimic certain physiochemical properties of MUC poypeptides. Chemical analogues may 5 be chemically synthesised or may be detected following, for example, natural product screening. Useful sources for screening for natural products include coral, reefs, sea beds, river beds, plants, microorganisms and aqua and antarctic environments. Still another aspect of the present invention is directed to 10 antibodies specific for MUC polypeptides and/or homologs thereof. In one embodiment, the anti-MUC antibody is M1 1.9. In another embodiment, the anti-MUC antibody is M12.15. A detailed method of anti-MUC antibody preparation is provided hereinafter. 15 In this regard, it will be understood that anti-MUC polypeptide antibodies may be produced by immunization with MUC polypeptides or MUC peptides. In particular, it is also likely that naturally-occurring anti-MUC antibodies may well have naturally arisen against MUC polypeptides. 20 In light of the foregoing, it will be appreciated that "anti-MUC antibody" as used herein is an antibody specific for, or at least binds to, a MUC polypeptide, irrespective of how the anti-MUC antibody was produced. The anti-MUC antibodies of the present invention may be useful as therapeutic or diagnostic agents. 25 For example, a MUC polypeptide or homolog can be used to screen for naturally occurring anti-MUC antibodies. These may occur, for example in some autoimmune diseases. Alternatively, anti-MUC antibodies can be used to screen for MUC polypeptides. Techniques for such assays are well known in the art and include, for example, sandwich assays and 30 ELISA. Knowledge of endogenous MUC polypeptide levels may be important for diagnosis of large bowel cancer or a predisposition to large bowel cancers WO 00/04142 PCT/AU99/00579 24 or for monitoring certain therapeutic protocols. This knowledge may also be important in other epithelial cancers such as cancer of the breast. Anti-MUC antibodies of the present invention may be monoclonal or polyclonal. Alternatively, fragments of antibodies may be 5 used such as Fab fragments. Furthermore, the present invention extends to recombinant and synthetic antibodies and to antibody hybrids. A "synthetic antibody" is considered herein to include fragments and hybrids of antibodies. The antibodies of this aspect of the present invention are particularly useful for immunotherapy and may also be used as a diagnostic 10 tool for assessing cancer development or cancer cell apoptosis or monitoring the program of a therapeutic regimum. For example, anti-MUC antibodies can be used to screen for endogenous MUC polypeptides. The latter would be important, for example, as a means for screening for levels of the MUC polypeptide in a cell extract 15 or other biological fluid or purifying the MUC polypeptide made by recombinant means from culture supernatant fluid. Techniques for the assays contemplated herein are known in the art and include, for example, sandwich assays and ELISA. It is within the scope of this invention to include any second 20 antibodies (monoclonal, polyclonal or fragments of antibodies or synthetic antibodies) directed to the first mentioned antibodies discussed above. Both the first and second antibodies may be used in detection assays or a first antibody may be used with a commercially available anti-immunoglobulin antibody. An antibody as contemplated herein includes any antibody specific 25 to any region of the MUC polypeptide. Both polyclonal and monoclonal antibodies are obtainable by immunization with the enzyme or protein and either type is utilizable for immunoassays. The methods of obtaining both types of sera are well known in the art. Polyclonal sera are less preferred but are relatively easily 30 prepared by injection of a suitable laboratory animal with an effective amount of a MUC polypeptide, or antigenic parts thereof, collecting serum from the WO 00/04142 PCT/AU99/00579 . 25 animal, and isolating specific sera by any of the known immunoadsorbent techniques. Although antibodies produced by this method are utilizable in virtually any type of immunoassay, they are generally less favoured because of the potential heterogeneity of the product. 5 The use of monoclonal antibodies in an immunoassay is particularly preferred because of the ability to produce them in large quantities and the homogeneity of the product. The preparation of hybridoma cell lines for monoclonal antibody production derived by fusing an immortal cell line and lymphocytes sensitized against the immunogenic preparation 10 can be done by techniques which are well known to those who are skilled in the art. The present invention contemplates a method for detecting a MUC polypeptide in a protein extract obtained from a mammal, said method including the step of forming a complex between an anti-MUC antibody and 15 a MUC polypeptide, and then detecting said complex. The presence of a MUC polypeptide may be determined in a number of ways such as by Western blotting and ELISA procedures. A wide range of immunoassay techniques are available as can be seen by reference to U.S. Patent Nos. 4,016,043, 4,424,279 and 4,018,653. These include both 20 single-site and two-site or "sandwich" assays of the non-competitive types, as well as in the traditional competitive binding assays. These assays also include direct binding of a labelled antibody to a target. Sandwich assays are among the most useful and commonly used assays and are favoured for use in the present invention. A number of 25 variations of the sandwich assay technique exist and all are intended to be encompassed by the present invention. Briefly, in a typical forward assay, an unlabelled antibody is immobilized to a solid substrate and the sample to be tested brought into contact with the bound molecule. After a suitable period of incubation, for a period of time sufficient to allow formation of an 30 antibody-antigen complex, a second antibody specific to the antigen, labelled with a reporter molecule capable of producing a detectable signal is then WO 00/04142 PCT/AU99/00579 . 26 added and incubated, allowing time sufficient for the formation of another complex of antibody-antigen-labelled antibody. Any unreacted material is washed away and the presence of the antigen is determined by measurement of a signal produced by the reporter molecule. The results may either be 5 qualitative, by simple observation of the visible signal, or may be quantitated by comparing with a control sample containing known amounts of hapten. Variations on the forward assay include a simultaneous assay, in which both sample and labelled antibody are added simultaneously to the bound antibody. These techniques are well known to those skilled in the art, 10 including any minor variations as will be readily apparent. In accordance with the present invention the protein extract might be a cell extract, tissue biopsy or possibly serum, saliva, mucosal secretions, lymph, tissue fluid and gastrointestinal fluid. The extract is, therefore, generally a biological sample. In the typical forward sandwich assay, a first antibody having 15 specificity for MUC or antigenic parts thereof, is either covalently or passively bound to a solid surface. The solid surface is typically glass or a polymer, the most commonly used polymers being cellulose, polyacrylamide, nylon, polystyrene, polyvinyl chloride or polypropylene. The solid supports may be in the form of tubes, beads, discs of microplates, or any other surface 20 suitable for conducting an immunoassay. The binding processes are well known in the art and generally consist of cross-linking covalently binding or physically adsorbing, the polymer-antibody complex is washed in preparation for the test sample. An aliquot of the sample to be tested is then added to the solid phase complex and incubated for a period of time sufficient (e.g. 2 25 40 minutes or overnight if more convenient) and under suitable conditions (e.g. from 4 0 C to 37 0 C) to allow binding of any subunit present in the antibody. Following the incubation period, the solid phase complex is washed and dried and incubated with a second antibody which is specific for a portion of the antigen (i.e. MUC). The second antibody is linked to a 30 reporter molecule which is used to indicate the binding of the second antibody to MUC.

WO 00/04142 PCT/AU99/00579 . 27 An alternative method involves immobilizing the target molecules in the biological sample and then exposing the immobilized target to specific antibody which may or may not be labelled with a reporter molecule. Depending on the amount of target and the strength of the 5 reporter molecule signal, a bound target may be detectable by direct labelling with the antibody. Alternatively, a second labelled antibody, specific to the first antibody is exposed to the target-first antibody complex to form a target first antibody-second antibody tertiary complex. The complex is detected by the signal emitted by the reporter molecule. 10 By "reporter molecule" as used in the present specification, is meant a molecule which, by its chemical nature, provides an analytically identifiable signal which allows the detection of antigen-bound antibody. Detection may be either qualitative or quantitative. The most commonly used reporter molecules in this type of assay are either enzymes, fluorochromes 15 or radionuclide containing molecules (i.e. radioisotopes) and chemiluminescent molecules. In the case of an enzyme immunoassay, an enzyme is conjugated to the second antibody, such as via glutaraldehyde or periodate amongst other means. As will be readily recognized, however, a wide variety 20 of different conjugation techniques exist, which are readily available to the skilled artisan. Commonly used enzymes include horseradish peroxidase, glucose oxidase, beta-galactosidase and alkaline phosphatase, amongst others. The substrates to be used with the specific enzymes are generally chosen for the production, upon hydrolysis by the corresponding enzyme, of 25 a detectable colour change. It is also possible to employ fluorogenic substrates, which yield a fluorescent product rather than the chromogenic substrates noted above. In all cases, the enzyme-labelled antibody is added to the first antibody-antigen complex, allowed to bind, and then the excess reagent is washed away. A solution containing the appropriate substrate is 30 then added to the complex of antibody-antigen-antibody. The substrate will react with the enzyme linked to the second antibody, giving a qualitative WO 00/04142 PCT/AU99/00579 _ 28 visual signal, which may be further quantitated, usually spectrophotometrically, to give an indication of the amount of antigen which was present in the sample. The term "reporter molecule" also extends to use of cell agglutination or inhibition of agglutination such as red blood cells on 5 latex beads, and the like. Also, fluorescent compounds, such as fluorescein and rhodamine, may be chemically coupled to antibodies without altering their binding capacity. When activated by illumination with light of a particular wavelength, the fluorochrome-labelled antibody adsorbs the light energy, 10 inducing a state of excitability in the molecule, followed by emission of the light at a characteristic colour visually detectable with a light microscope. As in the EIA, the fluorescent labelled antibody is allowed to bind to the first antibody-hapten complex. After washing off the unbound reagent, the remaining tertiary complex is then exposed to light of the appropriate 15 wavelength and the fluorescence observed indicates the presence of the antigen of interest. Immunofluorescene and EIA techniques are both very well established in the art. Other reporter molecules, such as radioisotope, chemiluminescent or bioluminescent molecules, may also be employed. The MUC genes of the present invention are likely to function 20 in cell adhesion, signal transduction, growth regulation, epithelial cell protection and/or immunological reactions. The classical gel-forming mucins function in protecting and lubricating epithelial tissues (particularly those of the respiratory and gastrointestinal tracts) by forming a layer of viscoelastic gel. These new mucins, MUCI I and MUC12, show structural similarity to 25 MUC1. MUC1 can be secreted, but unlike the classical mucins, it is primarily a type I transmembrane protein that interacts and complexes with other adhesion molecules, and is involved in signal transduction. MUC12 has an EGF growth factor-like domain, is likely to be a transmembrane protein and has a putative tyrosine phosphorylation site that may participate in 30 intracellular signalling. It is hypothesised that loss of MUC12 may be associated with poor prognosis in CRC.

WO 00/04142 PCT/AU99/00579 29 The isolated MUC nucleic acids of the present invention are, therefore, considered in one embodiment, to correspond to cancer suppressor genes. Suppression may mean total inhibition of any development of large bowel cancer or a limitation of the severity of or an 5 amelioration of the condition resulting from a large bowel cancer. The MUC nucleic acids of the present invention are also considered in another embodiment to be capable of modulating disease conditions such as CRC, BC, IBD, CF, asthma, chronic bronchitis, ulcerative colitis and/or Crohn's disease 10 Cystic fibrosis (CF) is an inherited disease of epithelial cell chloride ion transport that affects multiple organ systems. It is the most common cause of severe, progressive lung disease and exocrine pancreatic insufficiency in childhood. The cystic fibrosis transmembrane conductance regulator (CFTR) gene located on chromosome 7q22 encodes a large single 15 chain protein that forms a chloride channel. Virtually all of the morbidity and mortality associated with mutations in the CFTR gene causing cystic fibrosis arise from respiratory disease due to chronic infection and mucus obstruction. The precise mechanism of mucus accumulation in cystic fibrosis is controversial. Data suggest that CFTR malfunction may trigger mucin 20 secretion and alter mucus properties, and/or bacterial infection triggers the hypersecretion of mucin in CF patients. The gene of the present invention is expressed in the colon, pancreas, small intestine, and lung, all tissues where mucus obstruction occurs. Accordingly, aberrant expression of the genes may contribute to cystic fibrosis. 25 Aberrant mucin expression is also a recognised component of IBD. Inflammatory bowel disease is characterised by considerable alterations in glycosylation, sialyation and sulphation of glycoproteins. It is unclear whether the changes in mucus production are a cause or response to the disease. Susceptibility genes for inflammatory bowel disease have been 30 localised to chromosomes 3, 12 and 7q22. Accordingly, the MUC genes of the present invention are considered candidates for susceptibility genes for WO 00/04142 PCT/AU99/00579 . 30 IBD. Up or down regulation, or altered secretion of one of these mucins may influence the quality of colonic mucus and therefore the pathology of these diseases. Certain inherited forms of these genes may indicate a predisposition to IBD. 5 The identification of MUC genes and isolated MUC nucleic acids permits the generation of a range of therapeutic methods and compositions. Such therapeutics may modulate MUC gene expression and the activity of MUC polypeptides. Modulators contemplated by the present invention includes agonists and antagonists of MUC gene expression. 10 Antagonists of MUC gene expression include antisense molecules, ribozymes and co-suppression molecules. Agonists include molecules which increase promoter activity or interfere with negative mechanisms. Agonists of MUC include molecules which overcome any negative regulatory mechanism. Antagonists of MUC polypeptides include antibodies and 15 inhibitor peptide fragments. Another class of therapeutics may be designed to mimic or block intracellular signal transduction by MUC polypeptides. In accordance with the present invention, it is proposed that MUC functions as a suppressor of cancer development in the large bowel. Hereditary cancers arise with loss of the wild-type gene. In addition, 20 germline mutations underlying large bowel cancer are inactivated for the MUC genes and, therefore, hereditary cancers have no functional copy of the gene. Furthermore, sporadic large bowel cancers arise with somatic loss of both copies of the gene. The present invention extends to the use of modulating levels of expression of MUC genes or their translation products 25 in the context of cancers related thereto. Thus, the present invention contemplates a method of gene therapy of a mammal. Such a method utilizes a gene therapy construct which includes an isolated MUC nucleic acid ligated into a gene therapy vector which provides one or more regulatory sequences that direct expression of 30 said nucleic acid in said mammal. Such regulatory sequences may include a promoter, an WO 00/04142 PCT/AU99/00579 31 enhancer, a polyadenylation sequence, splice donor/acceptor sequences and translation termination and intiation sequences. Typically, gene therapy vectors are derived from viral DNA sequences such as adenovirus, adeno-associated viruses, herpes-simplex 5 viruses and retroviruses. Suitable gene therapy vectors currently available to the skilled person may be found in Robbins et al., 1998, Trends Biotechnol. 16 35, for example, which is herein incorporated by reference. If "anti-sense" therapy is contemplated, then one or more selected portions of a MUC nucleic acid may be oriented 3'45' in the gene 10 therapy vector. Administration of the gene therapy construct to said mammal, preferably a human, may include delivery via direct oral intake, systemic injection, or delivery to selected tissue(s) or cells, or indirectly via delivery to cells isolated from the mammal or a compatible donor. An example of the 15 latter approach would be stem-cell therapy, wherein isolated stem cells having potential for growth and differentiation are transfected with the vector comprising the MUC nucleic acid. The stem-cells are cultured for a period and then transferred to the mammal being treated. Delivery of said gene therapy construct to cells or tissues of 20 said mammal or said compatible donor may be facilitated by microprojectile bombardment, liposome mediated transfection (e.g. lipofectin or lipofectamine), electroporation, calcium phosphate or DEAE-dextran mediated transfection, for example. A discussion of suitable delivery methods may be found in Chapter 9 of CURRENT PROTOCOLS IN MOLECULAR 25 BIOLOGY (Eds. Ausubel et al.; John Wiley & Sons Inc., 1997 Edition), for example, which is herein incorporated by reference. For example, a MUC nucleic acid may be introduced into a cell to enhance the ability of that cell to survive, conversely, MUC antisense sequences such as 3-4 5' oligonucleotides may be introduced to decrease 30 the survival capacity of any cell expressing an endogenous MUC gene. In this regard, increased MUC expression or activity is WO 00/04142 PCT/AU99/00579 32 important in conditions of repressing cancer growth and/or development. Decreased MUC expression or activity may be important, for example, in the treatment of cystic fibrosis or the treatment of inflammatory bowel disease. Accordingly, the present invention contemplates a 5 pharmaceutical composition comprising a MUC polypeptide or a derivative thereof or a modulator of MUC gene expression or activity, inclusive of anti MUC antibodies. These components are referred to herein as the "active ingredients", and are suitably provided in combination with one or more pharmaceutically-acceptable carriers and/or diluents. 10 The pharmaceutical forms suitable for injectable use include sterile aqueous solutions (where water soluble) and sterile powders for the extemporaneous preparation of sterile injectable solutions. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and 15 fungi. The carrier can be a solvent or, for example, water, ethanol, polyol (for example, glycerol, propylene glycol and liquid polyethylene glycol, and the like) or suitable mixtures thereof as well as vegetable oils. The preventions of the action of microorganisms can be brought about by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic 20 acid, thirmersal and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin. 25 Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by filtered sterilization. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum 30 drying and the freeze-drying technique which yield a powder of the active ingredient plus any additional desired ingredient from previously WO 00/04142 PCT/AU99/00579 . 33 sterile-filtered solution thereof. When the active ingredients are suitably protected they may be orally administered, for example, with an inert diluent or with an assimilable edible carrier, or it may be enclosed in hard or soft shell gelatin capsule, or 5 it may be compressed into tablets, or it may be incorporated directly with the food of the diet. For oral therapeutic administration, the active compound may be incorporated with excipients and used in the form of ingestible tablets, buccal tablets, troches, capsules, elixirs, suspensions, syrups, wafers, and the like. Such compositions and preparations should contain at 10 least 1 % by weight of active compound. The percentage of the compositions and preparations may, of course, be varied and may conveniently be between about 5 to about 80% of the weight of the unit. The amount of active compound in such therapeutically useful compositions in such that a suitable dosage will be obtained. Preferred compositions or preparations 15 according to the present invention are prepared so that an oral dosage unit form contains between about 0.1 pg and 2000 mg of active ingredient. The tablets, troches, pills, capsules and the like may also contain the components as listed hereafter: a binder such as gum, acacia, corn starch or gelatin; excipients such as dicalcium phosphate; a 20 disintegrating agent such as corn starch, potato starch, alginic acid and the like; a lubricant such as magnesium stearate; and a sweetening agent such a sucrose, lactose or saccharin may be added or a flavouring agent such as peppermint, oil of wintergreen, or cherry flavouring. When the dosage unit form is a capsule, it may contain, in addition to materials of the above type, 25 a liquid carrier. Various other materials may be present as coatings or to otherwise modify the physical form of the dosage unit. For instance, tablets, pills, or capsules may be coated with shellac, sugar or both. A syrup or elixir may contain the active compound, sucrose as a sweetening agent, methyl and propylparabens as preservatives, a dye and flavouring such as cherry 30 or orange flavour. Of course, any material used in preparing any dosage unit form should be pharmaceutically pure and substantially non-toxic in the WO 00/04142 PCT/AU99/00579 34 amounts employed. In addition, the active compound(s) may be incorporated into sustained-release preparations and formulations. Pharmaceutically acceptable carriers and/or diluents include any and all solvents, dispersion media, coatings, antibacterial and antifungal 5 agents, isotonic and absorption delaying agents and the like. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, use thereof in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated 10 into the compositions. It is especially advantageous to formulate parenteral compositions in dosage unit form for ease of administration and uniformity of dosage. Dosage unit form as used herein refers to physically discrete units suited as unitary dosages for the mammalian subjects to be treated; each 15 unit containing a predetermined quantity of active material calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier. The specification for the novel dosage unit forms of the invention are dictated by and directly dependent on (a) the unique characteristics of the active material and the particular therapeutic effect to 20 be achieved, and (b) the limitations inherent in the art of compounding such an active material for the treatment of disease in living subjects having a diseased condition in which bodily health is impaired. The principal active ingredient is compounded for convenient and effective administration in effective amounts with a suitable 25 pharmaceutically acceptable carrier in dosage unit form as hereinbefore disclosed. A unit dosage form can, for example, contain the principal active compound in amounts ranging from 0.5 pg to about 2000 mg. Expressed in proportions, the active compound is generally present in from about 0.5 pg to about 2000 mg/mL of carrier. In the case of compositions containing 30 supplementary active ingredients, the dosages are determined by reference to the usual dose and manner of administration of the said ingredients. It is WO 00/04142 PCT/AU99/00579 . 35 also convenient to represent the effective amounts of active ingredients as an amount per kg body weight. For example, the present invention encompasses effective amounts for 0.005 pg/kg body weight at 2000 mg/kg body weight. 5 The pharmaceutical composition may also comprise genetic molecules such as a vector capable of transfecting target cells where the vector carries a nucleic acid molecule capable of modulating MUC gene expression or MUC polypeptide activity. The vector may, for example, be a viral vector. 10 From the foregoing, it is apparant that therapeutic methods and compositions of the invention are useful in the treatment of disease conditions associated with aberrant Mucin expression, altered properties of mucus or epithelial inflammatory processes involving Mucins. Preferably, the disease condition is selected from the group 15 consisting of colorectal cancer (CRC), cystic fibrosis (CF), inflammatory bowel disease (IBD), breast cancer (BC), Crohn's disease, ulcerative colitis, asthma and chronic bronchitis. More preferably, the disease condition is selected from the group consisting of colorectal cancer (CRC), cystic fibrosis (CF), 20 inflammatory bowel disease (IBD) and breast cancer (BC). although not limited thereto. The therapeutic methods of the invention may therefore be used to alleviate one or more symptoms of diseases or be used as prophylactic treatments to prevent, or reduce the likelihood of, said symptoms from occurring. 25 The present invention is further described by the following non limiting Examples. EXAMPLES EXAMPLE 1: Tissue Specimens Tissue specimens were collected from patients undergoing 30 surgery (Dukes' A n=5; Dukes' B n=5, Dukes C n=5, Dukes' D n=5). Colonic specimens were obtained from patients undergoing either colectomy or WO 00/04142 PCT/AU99/00579 36 partial hepatectomy for colorectal carcinoma. Samples of normal colonic mucosa, primary colon cancer, liver metastases (if present) and adjacent normal liver were rapidly excised from operative specimens, snap-frozen in liquid nitrogen and stored at -70 0 C until use. Care was taken to exclude 5 normal mucosal tissue from tumour samples. Junctional tissue specimens from four tumours of each Dukes' stage were randomly selected for in situ hybridisation. Tissues were fixed for 24-48 hours in 10% v/v buffered formalin, dehydrated in ethanol, cleaned in chloroform and embedded in parraffin wax. Biopsy specimens of normal colonic epithelium from four 10 distinct regions of the colon were collected via colonoscopy from each of three healthy individuals undergoing routine colonoscopic screening. Similarly, intestinal biopsies were obtained via colonoscopy from ten patients with inflammatory bowel disease. Specimens were snap-frozen and stored at -700 C until RNA was extracted as per Example 3 below. 15 EXAMPLE 2: Cell Lines and Culture Seven human colonic tumour lines were obtained: LIM1215, LIM2405, LIM1 863, LIMI 899 (Ludwig Institute, Melbourne, Australia), HT29 (ATCC HTB38), SW480 (ATCC CCL 228) and SW620 (ATCC CCL 227). LIM1215 and SW620 are each derived from CRC metastases. Cell lines were 20 maintained in RPMI 1640 with 10% v/v fetal calf serum, 2 mM glutamate, 25 mM HEPES, 60 mg/mI penicillin G and 100 mg/ml streptomycin sulfate and incubated in 5% v/v CO 2 and 95% v/v air at 37 0 C. Cultures were passaged twice weekly using standard techniques. The following breast carcinoma lines were included in this study: KPL-1 (a gift of Dr Junichi Kurebayashi, 25 Suzuki, Japan), MA1 1 (a gift of Dr Philip Rye, Oslo, Norway), BT 20, DU4475, MCF-7, MDA-MB-453, SK-Br-3, T47D, UACC-893, ZR-75-1 and ZR-75-30 (ATCC, Rockville, MD), and MDA-MB-435 and MDA-MB-468 (a gift of Dr. Janet Price, MD Anderson Cancer Center, Houston, TX). All breast cancer cell cultures were maintained in RPMI-1640 medium supplemented 30 with 10% fetal calf serum and 0.006% penicillin and 0.01% streptomycin with the following exceptions: DU-4475 in RPMI-1 640 with 20% FCS, KPL-1 was WO 00/04142 PCT/AU99/00579 37 maintained in DMEM with 5% FCS, MA1 1 in 1:1 Ham's F12:RPMI-1640 with 10% FCS, SK-Br-3 in McCoy's medium with 15% FCS, and UACC-893 in RPMI-1 640 with 15% FCS. EXAMPLE 3: RNA Extraction 5 Total RNA was isolated by the method of Chomczynski and Sacchi (Chomczynski et al., 1987, Anal. Biochem. 162 156). Cells were resuspended in RNA extraction buffer (4 M guanidinium isothiocyanate containing 25 mM sodium citrate, pH7.0, 0.5 % w/v sodium lauroyl sarcosine (SLS) and 0.1 M 2-mercaptoethanol). Tissue samples were homogenised in 10 RNA extraction buffer. Extracted RNA was dissolved in RNase-free water and the concentration and purity determined by spectrophotometry at 260 and 280 nm (Sambrook et al., Molecular Cloning, A Laboratory Manual. 2nd Ed. Cold Spring Harbour Laboratory Press. Cold Spring Harbour, NY, 1989). The integrity of the RNA was assessed by denaturing agarose gel electrophoresis 15 and samples transferred to HYBOND N (Amersham, Bucks, England) membrane by capillary blotting. EXAMPLE 4: DNA Sequencing Approximately 500 ng of DNA were employed in a cycle sequencing reaction with 2.5 pmol of primer and 4 pl of Dye terminator or 20 dRhodamine reaction mix (DNA Cycle Sequencing Kits, Perkin Elmer, Norwalk, CT,) in a total volume of 10 pl. Reaction mixes contained Amplitaq DNA polymerase, dNTPs and fluorescently labelled dideoxynucleotides (dye terminators). Cycling reactions were as follows: 25 cycles of denaturation at 96 0 C (30 s), primer annealing at 50*C (15 s) and extension at 60 0 C (4 min). 25 Unincorporated nucleotides were removed by ethanol precipitation. The reactions were analysed on a Model 373A automated DNA sequencer (Applied Biosystems) run by technical staff in the core sequencing facility of the Queensland Institute of Medical Research. EXAMPLE 5 Identification by Differential Display of Two cDNAs 30 Encoding Mucins Downregulated in Colorectal cancer WO 00/04142 PCT/AU99/00579 . 38 The differential display method was devised from the original technique described by Liang & Pardee, 1992, Science 257 967. Total RNA was isolated by the method as described previously. Reverse transcription was carried out using one of four anchored primers, T 12 MG, T 12 MC, T 12 MA 5 and T 1 2 MT (Operon Technologies Inc., Alameda, CA) and Superscript RNAse H- reverse transcriptase (Gibco BRL, Gaithersburg, MD). One arbitrary 1Omer primer (Operon Technologies Inc.) was selected at random to be employed in a PCR with the appropriate anchored primer. Two patients, 101 and 112, were analyzed simultaneously and duplicates of two separate 10 reverse transcription reactions electrophoresed on each gel. Gels were put down wet and autoradiographed for 1-3 days. DNA was removed from gel slices by boiling and reamplified by PCR. Bands were then cloned into pGEM-T (Promega Corporation, Madison, WI) and sequenced. Sequences were analysed by multiple sequence similarity searches using BLAST 15 algorithms (Altshcul et al., 1990, supra) accessed through the National Centre of Biotechnology Information (NCBI; http://www.ncbi.nlm.nih.gov). Differential display was performed on RNA from paired normal colonic mucosa and primary colorectal cancers. Using a PCR primer combination of T 12 MG and 10mer 5'-ACTTCGCCAC-3' (SEQ ID NO:7), 20 bands dd29 (MUC12) and dd34 (MUCI 1) were both amplified from normal colonic mucosal RNA of two patients and were consistently downregulated in the tumors from these patients in multiple PCR reactions (FIG. 1A). Following reamplification PCR, discrete bands of approximately 720 bp for dd29 and 530 bp for dd34 were isolated and cloned into pGEM-T. Sequence 25 analysis showed that both cDNAs were novel, with no match in any database accessed through the NCBI. Repetitive segments typical of mucin tandem repeats were observed in dd34. EXAMPLE 6: Northern Blot Analysis Northern blot analysis was performed on paired normal and 30 tumor total RNA extracted from the same patients employed in the differential display experiment. dd29 (MUC12) and dd34 (MUCI 1) were random primer- WO 00/04142 PCT/AU99/00579 39 labeled using a Megaprime DNA labeling system (Amersham, Aylesbury, UK) and hybridization performed at 65"C in buffer containing 7% SDS, 0.26 M Na 2

HPO

4 , 1 mM EDTA, 1% BSA. Northern blot analyses of dd29 (FIG. 1 B) and dd34 (FIG. IC) 5 with colonic total RNA used for the differential display reactions revealed a polydisperse signal beginning near the top of the gel for RNA isolated from normal colonic mucosa and no signal in tumor-derived RNA. Probe dd29 showed some cross-hybridization to ribosomal RNA. Polydispersity of signal is a hallmark of mucin RNA blots due to shearing of very high molecular 10 weight transcripts. EXAMPLE 7: Multiplex Semi-quantitative RT-PCR Multiplex semi-quantitative RT-PCR was performed on total RNA isolated from six colorectal cancer cell lines and from paired normal colonic mucosa and tumor colorectal cancer tissues from 20 patients, five of 15 each Dukes' stage. Informed consent was obtained from each subject after approval by the appropriate hospital Ethics Committee. PCR products were quantitated relative to a p 2 -microglobulin cDNA amplification control using densitometry. First strand cDNA synthesis was accomplished using 1 pg of total RNA. PCR amplification of cDNA was performed in a total volume of 25 20 pl containing 1 pl of the first strand cDNA synthesis reaction products, 2.5 pl 1 Ox Taq polymerase buffer (25 mM TAPS (tris-[hydroxymethyl]-methyl-amino propane-sulfonic acid, sodium salt) pH 9.3, 50 mM KCI), 2 mM dNTPs, 25 mM MgCl 2 , 20 pmol each of the forward and reverse primers, and 2.5 U Taq polymerase. Gene-specific forward and reverse primers for MUC12 and 25 MUC11 were designed to produce PCR products of 510 bp and 169 bp respectively. Primers for P 2 -microglobulin generated a PCR product of 247 bp (Gussow et al., 1987, J. Immunol. 139 3132). Primers were: MUC12F1; 5'-TGAAGGGCGACAATCTTCCTC-3' (SEQ ID NO:8); MUC12RI; 5'-TACACGAGGCTCTTGGCGATGTTG-3' (SEQ ID NO:9); 30 MUC11F1; 5'-CAGGCGTCAGTCAGGAATCTACAG-3' (SEQ ID NO:10); MUC11R1; 5'-GAGGCTGTGGTGTTGTCAGGTAAG-3' (SEQ ID NO:11); WO 00/04142 PCT/AU99/00579 40 p-21F; 5'-TGAATTGCTATGTGTCTGGGT-3' (SEQ ID NO:12); p-21R; 5'-CCTCCATGATGCTGCTTACAT-3' (SEQ ID NO:13); MUC12TOTF1;5'-AGCCAACCAGGCTCAGCTCT-3' (SEQ ID NO:14); and MUC12TOTRI;5'-GCTCACACAGTGGATGCTACC-3' (SEQ ID NO:15). 5 After an initial denaturation step of 94 0 C for 5 minutes, the amplification conditions were: 21 cycles of denaturation at 94 0 C (30 s) for MUC12, (24 cycles of denaturation at 94 0 C (30 s) for MUC1 1), annealing at 60*C (30 s) and extension at 72*C (30 s). PCR products were electrophoresed on 1.2% 1x TBE gels and photographed. 10 Due to the polydisperse signals obtained by Northern analysis, expression of MUC11 and MUC12 was examined in a range of colorectal cancer cell lines and tissue mRNAs by multiplex semi-quantitative RT-PCR. dd29 was not expressed in any of six colorectal cancer cell lines examined (FIG. 1 D). In contrast, dd34 showed a different pattern of expression, with 15 HT29, LIM1215, LIM1899, LIM1863 lines revealing very faint PCR products, and SW620 and SW480 lines showing relatively high levels of expression (FIG.1E). For tumor tissue-derived RNA, downregulation was defined as amplified band intensity less than 30% of that observed from paired normal colon tissue. dd29 was found to be downregulated or absent in 6/15 (40%) 20 tumors with paired normal samples, and at low levels in 3/5 (60%) Dukes' stage D samples (where normal colon was not available for comparison) (FIG.1F). dd34 was downregulated in the tumors of 12/15 (80%) paired samples and expressed at low levels in 4/5 (80%) Dukes' stage D samples. One of five Dukes' stage D samples showed relatively high levels of 25 expression of dd34 (FIG. 1 G). Significantly, 13/15 (87%) colorectal cancers showed downregulation of at least one of these mucin genes, with 5/15 (33%) showing downregulation of both genes. EXAMPLE 8: Differential Tissue Distribution of MUC11, MUC12 and MUC3 mRNAs 30 A human RNA "master blot" (Clontech, Palo Alto, CA, catalogue number 7770-1) with RNA from 50 different tissues and controls was used to WO 00/04142 PCT/AU99/00579 . 41 examine mucin gene expression. DNA fragments encoding dd29, dd34 and MUC3 (Genbank Accession No. M55405, a gift from Dr. Sandra Gendler, Mayo Clinic, Scotsdale, Arizona) were excised from vector and radiolabeled as described above. Hybridization was performed as per the manufacturer's 5 instructions. The master blot was reprobed with a radiolabeled p-actin cDNA as a loading control. Analysis of the tissue distribution of MUCI 1, MUC12 and MUC3 transcripts in RNA isolated from 50 different normal tissues showed a distinct pattern of expression for each gene (FIG. 5). MUC12 and MUCI I showed 10 highest expression in colon but had different patterns in other organs, mainly restricted to those of epithelial type. MUCII had a wider epithelial distribution than MUC12 which was restricted to expression in the colon, and weakly in the pancreas, prostate and uterus. Consistent with published findings (Van Klinken et al., 1997, Biochem. Biophys. Res. Comm. 238 143), 15 MUC3 was found to be predominantly expressed in the small intestine and at much lower levels in the colon. Interestingly, it was also present in the thymus. EXAMPLE 9: Extending the Sequences of dd29 and dd34 The strategy employed in the cloning of MUCI I and MUC12 is 20 shown in FIGS. 8A and 8B respectively. 9.1 Library Screening. A Xgtl 1 human fetal brain 5'-STRETCH PLUS cDNA library (Clontech, Palo Alto, CA) was screened using radiolabeled dd29 and dd34. X DNA was extracted and inserts were excised, cloned into pBSK- and 25 sequenced. 9.2 PCR to extend the sequence of dd34 by linking clones 2 and 15 Screening of the fetal brain library with clone dd34, yielded two new cDNA clones: clone 2 (1043 bp) and clone li5 (1045 bp). Clone dd34 was a perfect match to the middle of the larger clone 2. cDNA from clone li5, 30 however, was highly homologous but not identical to the cDNA from clone dd34. To ascertain whether these partial cDNAs arose from a single mRNA WO 00/04142 PCT/AU99/00579 42 transcript, RT-PCR was carried out using combinations of forward and reverse primers specific for each cDNA in an attempt to link them. RT-PCR was performed on total RNA extracted from normal colon in a stringent touchdown PCR using high fidelity DyNAzyme DNA polymerase (Finnzymes, 5 Espoo, Finland). Primer combination MUCII F1 and li5R (5' GGGAACACTGTGGTTTCAGTTGAG-3'; SEQ ID NO:16) yielded a PCR product of 2 kb demonstrating that these two cDNAs were derived from a single transcript. This product was cloned into pGEM-T and sequenced. 9.3 PCR library screening - to extend sequence of dd29 10 Forward and reverse primers for dd29 (dd29Fl and dd29R1) were used in combination with a T7 vector-derived primer in a stringent touchdown PCR to screen an ulcerative colitis (UC) plasmid library (a gift from Dr. Jonathon Fawcett, Queensland Institute of Medical Research, Brisbane, Australia). Amplified products were purified, cloned into pGEM-T 15 and sequenced. EXAMPLE 10: Sequence Analysis of dd29 (MUC12) The sequence of dd29 revealed that it was amplified as a result of priming of random 1 Omer at both ends of the PCR product and that it did not contain a 3' untranslated region (3'-UTR) or poly A tail. Screening of an 20 UC cDNA library with dd29-specific primers extended the sequence 840 bp in the 5' direction and 800 bp in the 3' direction to the poly A tail (Genbank Accession Number AF147790). To confirm contiguous cDNA sequence, primers MUC12TOTF1 and MUC12TOTR1 were designed to produce an expected PCR product of 1532 bp; primers corresponded to bases 230-250 25 and 1742-1762, respectively, in SEQ ID NO:6. In a stringent touchdown PCR amplification procedure an intense discrete product of the expected size was identified from normal colonic cDNA and cDNA from the Caco-2 colonic cancer cell line. This reaction confirmed the reported MUC12 cDNA sequence. 30 Conceptual translation of the composite MUC12 cDNA reveals the presence of serine/threonine and proline-rich degenerate tandem repeats WO 00/04142 PCT/AU99/00579 43 (FIG. 2) consistent with this protein being a member of the epithelial mucin family. The deduced 28 amino acid tandem repeat structure is shown in FIG. 2. Following the mucin-repeat domain, MUC12 contains two cysteine-rich EGF-like domains separated by a 150 amino acid non-mucin-like sequence 5 (amino acids 261-410) containing five N-glycosylation sites and a potential coiled-coil domain. The second cysteine-rich EGF-like domain is immediately followed by a putative transmembrane domain containing 26 hydrophobic or uncharged amino acids, and a cytoplasmic tail of 75 amino acids at the carboxyl terminus. 10 Sequence alignment of MUC12, human MUC3 (hMUC3), rat Muc3 (rMuc3), mouse Muc3 (mMuc3), human MUC4 (hMUC4) and rMuc4 is shown in FIG. 3. When aligned by the transmembrane amino acid sequences, MUC12 was found to have areas of significant homology to rMuc3, mMuc3 and hMUC3, including perfect conservation of eight cysteine 15 residues in the second EGF-like domain. With inclusion of three small gaps, each of these cysteines also align with those in rat and human MUC4. Interestingly, all six mucins contain a conserved EGF-like sequence of Cx(5)GPxCxCx(9)GExC. Furthermore, there is some (4 out of 8) conservation of the cysteine residues between MUC1 2 and the human and rodent MUC3 20 and MUC4 mucins in the first EGF-like domain. EXAMPLE 11: Sequence Analysis of dd34 (MUC11) Clone dd34 (544 bp) was also obtained as a result of priming of random 1 Omers at both ends of the PCR product. Screening of a Agtl 1 human fetal brain library yielded two positive plaques which hybridized to 25 dd34, clone li5 (1045 bp) and clone 2 (1043 bp). These two clones represented opposite ends of a 2.8 kb partial MUC11 cDNA sequence (Genbank Accession Number AF147791), the linking of which was established by PCR (see Methods). Conceptual translation of the MUC1 I composite is shown in FIG. 4. The entire 957 amino acid sequence consisted 30 of serine, threonine and proline-rich tandem repeats of 28 amino acids in length, consistent with it being derived from a large epithelial mucin. The WO 00/04142 PCT/AU99/00579 44 deduced tandem repeat structure and consensus repeat sequence for MUCI 1 is shown in FIG. 4. EXAMPLE 12: Chromosomal Localization of MUCh1 and MUC12 DNA fragments excised from dd29 (720 bp) and dd34 (530 bp) 5 were nick translated with biotin-14-dATP and hybridized in situ at a final concentration of 10 ng/pl to metaphases from two normal males. The fluorescence in situ hybridization (FISH) method was modified from that previously described (Callen et al., 1990, Ann. Genet. 33 219) in that chromosomes were stained before analysis with both propidium iodide as 10 counterstain and DAPI for chromosome identification. Images of metaphase preparations were captured by a cooled CCD camera using the CyroVision Ultra image collection and enhancement system (Applied Imaging Int Ltd, Sunderland, U.K.). Twenty metaphases from a normal male were examined for 15 hybridization to dd29 and dd34 probes. For both genes, all of the metaphases showed strong signal on one or both chromatids of chromosome 7, at band 7q22 (data not shown). A similar result was obtained using metaphases from a second normal male. EXAMPLE 13: Production of monoclonal antibodies reactive with 20 MUC11 and 12 The following peptides were conjugated to keyhole limpet haemocyanin (KLH) with the heterobifunctional cross-linking agent m maleimidobenzoy-N-hydroxysuccinimide ester using standard techniques (Harlow, E. & Lane, D. Antibodies: A Laboratory Manual, Cold Spring 25 Harbor, Cold Spring Harbor Laboratory, 1988, which is herein incorporated by reference): MUC11: CFHSRPASTHTTLFTED (SEQ ID NO: 17); corresponding to part of the degenerate tandem repeat region, specifically amino acid residues 690-705 deduced from the partial cDNA MUCI 1 30 clone, with an N-terminal cysteine residue added for conjugation); WO 00/04142 PCT/AU99/00579 _ 45 MUC12: TYRNFTEKMNDASSQEC (SEQ ID NO: 18); corresponding to part of the N- glycosylated region, specifically amino acid residues 286-302 deduced from the partial cDNA MUC12 clone, with a C-terminal cysteine residue added for 5 conjugation). One Balb/c mouse was immunised with each KLH-conjugated peptide as per the following protocol: Day 0: KLH-conjugated peptide was diluted to 100 pg/mL in phosphate buffered saline (PBS) and mixed with an equal 10 volume of complete Freund's adjuvant (CFA). Each mouse was injected intra-peritonealy with 0.5 mL of this mixture. Day 14: Each mouse was immunised as above but peptide was mixed with incomplete Freund's adjuvant (IFA). Day 33: Each mouse was immunised as on day 14. 15 Day 43: Each mouse was bled from the tail to assess antibody production by ELISA (see below). Day 53: Each mouse was injected intra-venously with 100 pL of peptide at 100 pg/mL in PBS without adjuvant, and with 100 pL mixed with IFA intra-peritonealy. 20 Day 56: Mice were euthanased, and the spleen removed for fusion with myeloma cells. Splenocytes were fused to Ag8 mouse myeloma cells at a ratio of 5:1 with polyethylene glycol using established methods (Harlow & Lane, supra). 25 Specific antibody producing clones were screened by a solid phase antigen antibody capture ELISA with the immunizing peptides bound to polystyrene assay plates using established methods (Harlow & Lane, supra). Positive clones were expanded, retested for specific antibody production and recloned by limiting dilution. Clones were further tested for 30 reactivity with paraffin embedded normal colonic mucosa. 13.1 MUCI I and MUC12 reactive hybridomas WO 00/04142 PCT/AU99/00579 46 Two hybridomas, one reacting with each of MUC1 1 and MUC12 peptides and with paraffin embedded colonic sections are described in Table 2. 13.2 Immunohistochemical detection of MUCI1 and MUC12 in 5 normal colonic epithelium usinq antibodies M11.9 and M12.15 Paraffin sections (4 pm) of normal colonic epithelium were dewaxed with xylene, hydrated in a graded series of ethanol to water and treated with 0.1 U/mL neuraminidase (Boehringer, Germany) in 50 mM Na acetate, 150 mM NaCl, 100 mM CaCl 2 buffer, pH 5.5 for 1 hr at room 10 termperature to remove sialic acid groups. Sections were then treated with 1% H 2 0 2 , 0.1% NaN 3 in Tris buffered saline (TBS) for 10 min to quench endogenous peroxidase activity, and non-specific protein binding blocked with 4% skim milk in TBS for 15 min. Monoclonal antibodies M11.9 and M12.15 were semi-purified by PEG precipitation and diluted to 5-50 pg/mL 15 in TBS/50% non-immune goat serum and incubated for 2 hours overnight at room temperature. Sections were washed once with I % TX-1 00 in TBS for 5 min and then twice in TBS for 5 min. Sections were incubated for 30 min at room temperature with pre-diluted biotinylated goat anti-mouse immunoglobulins (Zymed, USA) and then washed as above. Sections were 20 then incubated for 15 min at room temperature with pre-diluted streptavidin conjugated horseradish peroxidase (Zymed Laboratories) and then washed as above. Peroxidase activity was detected using 10 mg/mL 0.05% diaminobenzidine, 0.03% H 2 0 2 in Tris saline, pH 7.6. Sections were counterstained with haematoxylin, dehydrated with ethanol, cleared with 25 xylene and mounted in DePeX. M1 1.9 reacts strongly with colonic epithelium, primarily with columnar cells of the surface epithelium (see FIG. 9A). Both goblet and columnar cells deep in the crypts are not stained by this antibody (see FIG. 9A). In surface epithelial columnar cells M1 1.9 reacted with the perinuclear 30 cytoplasm, lateral cell membranes and most strongly as granular staining in the subapical cytoplasm (FIG. 9B). This localisation suggests reactivity with WO 00/04142 PCT/AU99/00579 47 precursor in the rough endoplasmic reticulum (perinuclear staining), reactivity with mature mucin on the lateral membranes at columnar cell junctions with other cells, and reactivity with processed mature mucin in granules for apical secretion or incorporation into the apical cell membrane. This pattern of 5 reactivity is distinct from that seen for other known mucin core proteins. M12.15 also reacts strongly with colonic epithelium, and like M1 1.9 it reacts primarily with columnar cells of the surface epithelium (see FIG. 9C). However, M12.15 gave a more diffuse cytoplasmic staining pattern than that seen with M1 1.9, although, like M1 1.9, the strongest staining was 10 in the apical cytoplasm. Immunohistochemistry in normal colonic mucosa with these antibodies demonstrates protein expression of the MUC1 I and MUC12 gene, supporting the mRNA studies. The co-expression of MUC1 1 and MUC12 in normal colon is also consistent with the RT-PCR data showing similar levels 15 of relative expression of these two mucin genes in different regions of the intestinal tract. EXAMPLE 14: Expression of MUC11 by in situ hybridization 14.1 Methods Optimisation of conditions for in situ hybridisation, outlined 20 below, was based upon published techniques (Rex & Scotting, 1994, Biochemica 3 24, which is herein incorporated by reference). Riboprobes were made by in vitro transcription of DNA with SP6 and T7 RNA polymerases and incorporation of a digoxigenin-labelled uridine triphosphate (DIG-UTP). The orientation of inserts in pGEM-T was established by 25 sequencing. Insert in the antisense direction and thus complementary to RNA template was the hybridisation probe and insert in the sense direction was used as a negative control. I mg of purified linearised plasmid pGEM-T was labelled in the presence of 1/10 volume 10 x transcription buffer, 1/10 volume 10 x NTP mix (1 mM ATP, CTP, GTP, 0.65 mM UTP, 0.35 mM DIG-UTP), 30 1OU RNase inhibitor and 40U of either SP6 or T7 RNA polymerase. The reaction was carried out at 37 0 C for 2 hours and terminated by addition of 2 WO 00/04142 PCT/AU99/00579 48 pl of 0.2M EDTA. Probes were ethanol precipitated with 1/11 volume 4M LiCI and placed at -200C for 2 hours. They were then centrifuged at 12,000 g for 30 min at 40C. Pellets were washed with 70% ethanol, air-dried for 10 min and resuspended in 100ml of RNase-free water. 5 Paraffin-embedded junctional tissue specimens were sectioned at 4 pm onto sterile water and affixed to Vectabond-treated slides (Vector Laboratories). Sections were dewaxed in xylene, rehydrated and then incubated for 5 min in 0.2 N HCI. HCI treatment contributes to an improvement in the signal to noise ratio by extraction of proteins and partial 10 hydrolysis of target sequences. Slides were washed in sterile water for 5 min, followed by 5 min in PBT (PBS and 0.1% Tween 20). Sections were then incubated in proteinase K (5 mg/ml) at 370C for 15 min and washed briefly in 3 x PBT. They were fixed in 4% paraformaldehyde for exactly 20 min and prehybridised for 4 hours at 70*C in hybridisation buffer (50% formamide, 5 15 x SSC, 1% SDS, 500 mg/mL tRNA, 50 mg/mL heparin). Denatured probe (0.5 mg/section) was added to hybridation buffer and sections hybridised overnight at 700C. Sections were washed in 2 x wash solution 1 (50% formamide, 5 x SSC, 1% SDS) at 650C followed by 2 x washes in wash solution 2 (50% 20 formamide, 2 x SSC) also at 650C. Sections were then incubated with anti digoxygenin-AP antibody at 1/2000 in PBS overnight at 400C. Excess antibody was removed by 3 x 20 minute washes in PBT. Sections were then washed 2 x 20 minute in NTMT buffer (100 mM Tris, (pH 9.5), 50 mM MgCl 2 , 100 mM NaCl, 0.1% Tween 20, 2 mM levamisole). 25 Hybridisation was visualised with NBT and BCIP overnight at room temperature. The reaction was stopped by immersion of slides into 1 x TE and sections lightly counterstained in eosin. Sections were then dehydrated through ethanols of increasing concentration to xylene and mounted in DePeX. Slides were photographed within 3 days due to fading of the signal 30 with time. 14.2 Detection of MUC 11 mRNA by in situ hybridization WO 00/04142 PCT/AU99/00579 _ 49 Intense signal for MUCI I was observed in the columnar cells of the surface epithelium in all specimens of the normal colon. However, it was not possible to conclusively identify positive signal in the goblet cells of the colonic epithelium. Transcripts for MUCI I were not detected in adjacent 5 carcinoma of several junctional tissue specimens (an example is shown in FIG. 9D), thus confirming the findings of the differential display and Northern blot analyses. EXAMPLE 15: Expression of MUC11 and MUC12 in normal colon by RT-PCR 10 The results of RT-PCR experiments to determine the expression patterns of MUC11 and MUC12 genes in normal colonic epithelium are shown FIG. 10. MUCI I and MUC12 are predominantly expressed in the colon, although the data in FIG. 10 show that in fact their levels of expression vary 15 within the colon. In this regard, a progressive increase (3-4 fold) in the expression of both MUCI I and MUC12 was seen from the right colon to the rectum. EXAMPLE 16: Expression of MUC11 and MUC12 in CRC by RT PCR and Northern hybridization 20 The expression patterns of MUC1 I and MUC12 in CRC were investigated by RT-PCR, and the results are shown in FIG. 11. After 40 rounds of amplification, MUC11 expression was observed in all CRC cell lines under investigation. Similarly, MUC12 expression was observed in all cell lines, although two cell lines, SW620 and SW1 16 revealed low levels of 25 expression. These observations, together with the downregulation data, show that although these genes are downregulated in CRCs, they are still detectable in CRC cell lines. In contrast to the normal gastrointestinal tract and IBD tissues, the expression of MUC11 and MUC12 in CRCs and in CRC 30 cell lines show patterns of expression distinct form each other. Referring to FIG. 14, the results of Northern analysis with a WO 00/04142 PCT/AU99/00579 50 dd34 (MUCI I) probe showed that in nucleic acid extracts obtained from colonic tissue of four (4) of the (6) CRC patients tested, the level of MUCI I mRNA expression was lower relative to normal colonic tissue from the same patients. Similarly, MUC12 mRNA was downregulated in three (3) of five (5) 5 CRC patients (data not shown). Such quantitative (e.g. downregulation of these genes and differential downregulation expression patterns of MUCI 1 and MUC12) and also qualitative changes of these genes, e.g. mutations, could be used for diagnostic and prognostic testing in CRC. 10 EXAMPLE 17: Expression of MUC11 and MUC12 in IBD by RT-PCR The expression patterns of MUCI I and MUC12 in IBD were investigated by RT-PCR, and the results are shown in FIG. 12. Cytokeratin 20, (CK20) a colonic epithelial marker, was employed as a loading control due to the variable epithelial content of IBD tissues. 'N' denotes tissues 15 which appear macroscopically normal and 'D' refers to tissues reported to have IBD. 'CA' refers to the caecum, 'CO' the colon, 'LC' the left colon, 'TC' the transverse colon, 'RS' the recto-sigmoid colon, 'Sl' the small intestine, 'IL'denotes the ileum and 'IP' an ileal pouch. Two patients, patient 1 and patient 4, show 3-4 fold upregulated 20 expression of MUC1 I and MUC12 in diseased tissues, compared with the same intestinal region observed in the 3 normal controls. Patient 6, who has a history of severe ulcerative colitis in the right colon, also revealed approximately 3-fold upregulated expression of MUC11 and MUC12 compared to the right colon observed in the normal controls. 25 There is coordinate regulation of Mucin expression in the normal gastrointestinal tract as well as in IBD tissues and upregulation of both Mucin genes was observed in 3/10 patients. Given the documented quantitative changes in the expression of MUCII and MUC12, their expression levels may form the basis of useful diagnostic and prognostic 30 testing for this disease. Qualitative changes in these genes, eg. mutations may also be useful markers for IBD.

WO 00/04142 PCT/AU99/00579 51 EXAMPLE 18: Expression of MUC11 and MUC12 in BC by RT-PCR The expression patterns of MUC 11 and MUC12 in BC tissue were investigated by RT-PCR, and the results are shown in FIG. 13. After 40 rounds of amplification, MUCI I expression was identified in all breast cancer 5 cell lines under investigation; at low levels in BT-20, DU4475, MDA-MB-435 and ZR-75-30 cell lines and at higher levels in the remaining nine cell lines. Eight of the cell lines showed MUC11 expression higher than the normal colonic cDNA positive control. MUCI I is clearly highly expressed by most breast cancers and may impact upon the behaviour of the breast cancer 10 cells. MUCI I may also be secreted by breast cancers and detection in serum could form the basis of diagnostic and prognostic testing for breast cancer. MUC12 expression was only readily identifiable in one breast cancer cell line, MCF7, although faint bands were observed for BT20, KPL-1 and MAI 1 cell lines. 15 EXAMPLE 19: Experimental Summary Differential display has been used to identify two partial cDNAs, which encode novel colonic mucin-like proteins. Expression of both cDNAs, designated MUCI I and MUC12 by the Human Nomenclature Committee, was commonly downregulated in colorectal cancers. 20 MUC11 and MUC12 were mapped by FISH to chromosome band 7q22. The location of another mucin gene, MUC3, at 7q22, suggests the identification of a new cluster of mucin genes at this locus. Interestingly, four genes encoding gel-forming mucins are found in a cluster on chromosome 11 and these genes appear to have originated from a common 25 ancestral gene. While the mucin cDNAs mapped to 7q22 most likely represent separate genes, it is also possible that they are produced as a result of alternative mRNA splicing from a single, large mucin gene. Northern blot analysis for MUCI 1, MUC12 and MUC3 shows that these encode large transcripts, estimated to be greater than 12 kb. 30 Multiple tissue RNA analysis showed no cross-reactivity between MUCI1, MUC12 or MUC3. MUC11 and MUC12 showed WO 00/04142 PCT/AU99/00579 52 predominant expression in the colon, while MUC3 was predominantly expressed in the small intestine and at very low levels in the colon. This expression pattern constitutes an important point of distinction between MUCI I and MUC12 genes of the present invention and MUC3. Furthermore, 5 the sequences of MUC11 and MUC12 are not homologous with any other human mucin genes, but show some degree of similarity within their variable tandem repeat regions to each other (71 % over 653 bp). However, their clear differential expression patterns in normal and tumor tissues as well as tumor cell lines, show that they are distinct from each other, and from MUC3. 10 While both MUC11 and MUC12 contain variable repeat regions typical of mucins, MUC12 is putatively a transmembrane mucin with features suggesting an involvement in growth regulation, a largely unrecognized function in human mucins. MUC12 is only the fourth human membrane anchored epithelial mucin to be described to date, along with MUC1, MUC3 15 and MUC4. MUC1 has been shown to be involved in cell signaling via multiple tyrosine phosphorylation sites on its highly conserved cytoplasmic tail (Zrihan-Licht et al., 1994, FEBS Lett. 356 130). At its carboxyl terminus, MUC12 possesses a cytoplasmic tail containing a YNNF sequence (amino acids 557-560 in FIG. 2) which is similar to motifs recognized by SH2 20 domain-containing proteins (Songyang et al., Mol. Cell. Biol. 14 2777), suggesting that MUC12, like MUC1, may be involved in signal transduction. The deduced amino acid sequence of the partial MUCI 1 cDNA was composed entirely of serine/threonine-rich tandem repeats. There is a similarity between the tandem repeat consensus sequences of MUC1 1 (FIG. 25 4) and MUC12 (FIG. 2) and these also show limited homology to the MUC3 repeat (ITTETTSHSTPSFTSS). These similarities are consistent with evolution from a common ancestral gene. MUCI I is more widely expressed than MUC12 and MUC3 however, with RNA detected in gastrointestinal, respiratory, reproductive and urinary tracts, and unexpectedly in the liver and 30 thymus. The physiological roles of MUC11 and MUC12 in colonic WO 00/04142 PCT/AU99/00579 53 epithelium are unknown. MUCI I and MUC12 are commonly downregulated in colorectal cancer suggesting they may play a role in epithelial cell growth modulation and/or differentiation. At present, it is not possible to comment on whether downregulation of these genes is related to stage of tumor 5 progression, as only 20 patients were analyzed in this study. However, downregulation appears to be so frequent, that it may be an early event in tumorigenesis. Given the co-localization of the MUCI 1 and MUC12 genes on chromosome 7q22, it is possible that their expression is co-ordinately regulated and hence they are simultaneously downregulated in a large 10 proportion of colorectal cancers. The effect of downregulation of these mucins on normal colonic epithelial cells could be substantial. Mucins are believed to protect epithelial cells from attack by pathogenic organisms and from mechanical and chemical damage. Therefore, reduced expression of these mucins could expose colonic epithelial cells to the harsh environment 15 of the intestinal lumen. Furthermore, loss of a transmembrane mucin such as MUC12 may also contribute to loss of critical cell signaling. The location of these two novel mucin genes on chromosome 7q22 may have significance for two non-malignant epithelial diseases where aberrant mucin expression and/or function is a recognized component of 20 pathology, namely, inflammatory bowel disease and cystic fibrosis. Susceptibility genes for inflammatory bowel disease have been located to chromosomes 3,12 and 7q22 (Satsangi et al., 1996, Nature Genet. 14 199). Thus, MUC1 I and MUC12 must be considered candidates for involvement in inflammatory bowel disease given their chromosomal localization, 25 expression in normal colon, and the documented alterations in mucins in this disease (Rhodes, 1997, QJM 90 79). Mucins may also play a role in cystic fibrosis as patients with the same CFTR gene mutation do not demonstrate exactly the same phenotype in terms of mucus obstruction. The existence of modifier genes has been postulated and mucin genes are obvious 30 candidates (Harris & Reid, 1997, J. Med. Genet. 35 82). A murine Mucin gene that shows C-terminal homology with MUC12 has recently been shown WO 00/04142 PCT/AU99/00579 . 54 to be a major constituent of obstructive mucus in the gastrointestinal tract of mice with CF (Parmley et al., 1998, J. Clin. Invest 102 1798). The CFTR gene lies in the adjacent chromosome band (7q31) to the MUC3, MUC11 and MUC12 genes. While the significance of these 5 findings is not clear, MUC1 I and MUC12, which are expressed in many of the tissues affected by cystic fibrosis, should be considered as candidate modifier genes involved in the aetiology of this disease. Mucins are encoded by large genes which have proved difficult to clone by conventional methods due to the repetitive nature of their tandem 10 repeat regions. Hereinbefore, the present inventors have unexpectedly identified by differential display two partial cDNAs which represent novel mucin genes that are predominantly expressed in colonic epithelium, both of which are downregulated in colorectal cancer. In this regard, MUC1 I and MUC12 differ from the other mucin gene located on chromosome 7q22, 15 MUC3. These findings together with the sequence homology between the MUC12 EGF-like domain and EGF receptor-binding growth factors, suggest MUC1 and MUCI2 may function as growth regulators in colonic epithelium. Downregulation of these two novel mucin genes could be an important and previously unrecognized step in colorectal carcinogenesis. 20 Those skilled in the art will appreciate that the invention described herein is susceptible to variations and modifications other than those specifically described. It is to be understood that the invention includes all such variations and modifications. The invention also includes all of the steps, features, compositions and compounds referred to or 25 indicated in this specification, individually or collectively, and any and all combinations of any two or more of said steps or features.

WO 00/04 142 PCT/AU99/00579 55 LU ( C a () c =3 Ul) a) ~ U) a () (1 ) a) ou m~ cu . . E c: E EE E E EEEEE E o z z z z z Z Z Z Z z Z Zz ~~ a)0 ~ C -u Cu ~cu FD, E u -o =s cu= 11 CUc )a) 2- - L >1 D cu cn - =3 U).CrUE CO COU 0) CL U) c J ~ 0) z L) 00 ) U)( ) wUa cu CC O~_Q U o C: U) C a) ~ U) Z~~ > L >-~ C C -T co LU~L o) 00- > _ .. ...... C C ... .. .. .......... m .. ......c WO 00/04142 PCT/AU99/00579 56 C (D 0 2 0) CU 0 a a. U) -. . > a) .0 >U) (U 0) 0~~~~ E E EE E Z~C O 0 z z z z Z Z Z z z z a) c) U U a)Ua ) 0 ca c C .c - C L a)Cx a o o ) r_ >e 5 :,L 2 - ) a). > f 0 a U) a) 0)0 m 0 E (D:3C 0 a) E) a)3 ) Ej C U - a ' a)U a)) ) a) E ) a a ) - L o =v na ) cn _c* a) ru C zZ) -C E) 0 a) > E0 E a) 0 0 m a) aa ) 0U C:0 0 ii ca 0 0)C: 0 0C U ? a :3E WO 00/04 142 PCT/AU99/00579 57 a) Cl. C3 CL 0) a) aa)U0. Co3 CD O) CE Ca (U a) - U) ' C- ) - ) .0 .r C o Z E<zZ zZ z z z z z a) ) a) a) aI) a) c a) a) C c . c C C a) C ) ) U) _u C 0)3,~ - > >N -C C2 -C Ur ) U) >1 - 0) >, CL I-- U) zz -C o a) CD a) Nb ~ ~ E - )-~ X o o 0 E~ -5 2 o2c a)~( cu EU0 -L E 6 c a) z z C) 0000000 0000000 U) cnU> a) U C) a ) C U C U ) Ca ) ~ c C a) ~ ~ a) a ) a _ cu a) Z) mU CC C C a-~ =: *(: CU aa)U) ) U) 4 CU _c -c~ a a) C a) a) E > Z E a) a a) E ) E E E E a) E, WO 00/04142 PCT/AU99/00579 58 LU( -DQ 0 0) ca *~2 E a a o o n - ~ E E E z zz zz zZ z zE E Z0 ZOEO U) a) a) c a) (D a) a) C U 4- r_ a) a) CL c)~~U Z 5 a) 0 ) P 0 -C 0 )0 )a > ~ , > U) a 0 ZZm 0 ca_~c < a) 2 U) U) .L ON 0-0u 0~ ZC a)ZZ - cu~ c a U cu 51,U) : U cu u ) ) > a ,JJ~0 E- U U o6 z z ca. U)cD U)x L 4 .fi c U) C (D a) 0 m m - )UC c 6 Ca E E u E E E V E -Eo - E cuzU Z~~ a) a ) a~5 - ) a) 2 ) a) Z ca

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WO 00/04 142 PCT/AU99/00579 59 CU C ) CU C 0 C S (D cn ) 0 0 ) ) =3 C l a ) Cu:'0 ~CD (I ) - Ea)C > T C : ) a) -E a)' a) -u a)a :, > - 0 ) >N E: ) C 0) a) cc E .E a oo c~~c Z c -C - ) 0 a) 0- -U~ ac U U () ~ _L CC a) a) 0 CU -r- -r a ) .9 ) - U U a E ~~a E -rr E' C CCC ~Z U )E E E 0- Ec o ~ _r C -- J zz0 L )a E 0 =

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WO 00/041 42 PCT/AU99/00579 60 -C ) a) c 0 ~ CL -C a) a) a)U) cc~ _: U)a) M 0 CL a)- - c - (D 0~ 0 0o o~ C -~ X- 4- E U C:: :2 1 0 ZL a)j U)0 r- a~ ) o E 'o ) a)z )c oE E a' E>~ E E U)c -CU > a- c > E c Cu 0 C C acu a) .4-. C u Z - 0 c w i a > 0) (D 0 -C x ~ ~ E CN z C a)~ - ~ E' C.) WO 00/04142 PCT/AU99/00579 61 TABLE 2 Hybridoma, immunising isotype Peptide i mno peptide reactivity histocheia reactivity with colon Ml11.9 MUC1 1 1gM +++ Reacts with paraffin embedded tissue, reactivity enhanced by pre-treatment of sections with neurami nidase which removes sialic acid groups. M12.15 MUC12 1gM +++ Reacts with paraffin embedded tissue, reactivity enhanced by pre-treatment of sections with neuraminidase which removes sialic acid groups.

Claims (32)

1. An isolated MUC nucleic acid corresponding to a MUC gene located on human chromosome 7q22, or a mammalian chromosome structurally or functionally equivalent thereto, which MUC gene is normally predominantly expressed in the colon.

2. The isolated MUC nucleic acid of Claim 1 which comprises a nucleotide sequence encoding an amino acid sequence which comprises SGLSEESTTSHSSPGSTHTTLSPASTTT(SEQ ID NO :1).

3. The isolated MUC nucleic acid of Claim 2, wherein the nucleic acid comprises a nucleotide sequence encoding an amino acid sequence according to SEQ ID NO:3.

4. The isolated MUC nucleic acid of Claim 2, wherein the nucleic acid includes a sequence of nucleotides according to SEQ ID NO: 2.

5. The isolated MUC nucleic acid of Claim 1, wherein the nucleic acid which comprises a nucleotide sequence which encodes an amino acid sequence whuch comprises SGLSQESTTFHSSPGSTETTLAPASTTT (SEQ ID NO: 4).

6. The isolated MUC nucleic acid of Claim 5, wherein the nucleic acid comprises a nucleotide sequence which encodes an amino acid sequence according to SEQ ID NO:6.

7. The isolated MUC nucleic acid of Claim 5, wherein the nucleic acid includes a sequence of nucleotides according to SEQ ID NO: 5.

8. A MUC nucleic acid homolog which hybridizes to the isolated MUC nucleic acid of any one of Claims 2-7 under conditions of at least low stringency.

9. A MUC nucleic acid homolog which has at least 60% nucleotide sequence identity with the isolated MUC nucleic acid of any one of Claims 2-7.

10. An isolated MUC polypeptide having an amino acid sequence according to SEQ ID NO: 3.

11. An isolated MUC polypeptide having an amino acid sequence WO 00/04142 PCT/AU99/00579 . 63 according to SEQ ID NO: 6.

12. An isolated MUC polypeptide homolog which has at least 60% amino acid identity with the MUC polypeptide of Claim 10 or Claim 11.

13. An antibody specific for the MUC polypeptide or MUC polypeptide homolog of any one of Claims 10-12.

14. An antibody according to Claim 13 which is a monoclonal antibody.

15. A monoclonal antibody according to Claim 14, which monoclonal antibody is selected from the group consisting of M1 1.9 and M12.15.

16. A method of detecting the MUC polypeptide of Claim 10 or Claim 11, including the steps of: (i) obtaining a sample from said mammal; (ii) forming a complex between said MUC polypeptide, if present in said sample, and an anti-MUC polypeptide antibody; and (iii) detecting said MUC polypeptide in said complex.

17. The method of Claim 17, wherein the antibody is selected from the group consisting of M11.9 and M12.15.

18. A method of detecting a MUC gene or a MUC gene transcript including the steps of: (i) obtaining a nucleic acid extract from said mammal; (ii) forming a hybrid nucleic acid comprising a MUC gene or a MUC gene transcript if present in said sample, and a corresponding isolated MUC nucleic acid according to Claim 1, or a portion thereof; and (iii) detecting said hybrid nucleic acid.

19. The method of Claim 18, wherein the isolated MUC nucleic acid has a nucleotide sequence selected from the group consisting of SEQ ID NO:2 and SEQ ID NO:5.

20. A method of detecting a MUC gene or a MUC gene transcript WO 00/04142 PCT/AU99/00579 64 including the steps of: (i) obtaining a nucleic acid extract from said mammal; (ii) using one or more primers, each having a nucleotide sequence corresponding to a distinct portion of the isolated MUC nucleic acid of Claim 1, together with a polynucleotide sequence amplification technique, to produce a MUC gene amplification product from said extract; and (iii) detecting said MUC gene amplification product.

21. The method of Claim 20, wherein the one or more primers is selected from the group consisting of SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 14 and SEQ ID NO:15.

22. The method of Claim 21, wherein the polynucleotide sequence amplification technique is RT-PCR.

23. Use of the isolated MUC nucleic acid of Claim 1, or a portion thereof, to detect a polymorphism, mutation, deletion, truncation and/or expansion in a corresponding MUC gene or MUC gene transcript.

24. A pharmaceutical composition comprising a pharmaceutically acceptable amount of the MUC polypeptide of Claim 10 or Claim 11, together with a pharmaceutically-acceptable carrier and/or diluent.

25. A pharmaceutical composition comprising a pharmaceutically acceptable amount of an anti-MUC antibody according to any one of Claims 13-15, together with a pharmaceutically-acceptable carrier and/or diluent.

26. A method of treating of a mammal suffering from a disease condition, said method including the step of administering to said mammal a pharmaceutical composition according to Claim 24 or Claim 25 to thereby alleviate or prevent one or more symptoms of said disease condition in said mammal.

27. A method of gene therapy of a mammal suffering from a disease condition, said method including the step of administering a gene therapy construct to said mammal, said gene therapy construct comprising WO 00/04142 PCT/AU99/00579 65 the isolated MUC nucleic acid of Claim 1, or a portion thereof, to thereby alleviate or prevent one or more symptoms of said disease condition in said mammal.

28. The method of Claim 27, wherein the isolated MUC nucleic acid has a nucleotide sequence selected from the group consisting of SEQ ID NO:2 and SEQ ID NO:5.

29. The method of any one of Claims 26-28, wherein said disease condition is associated with aberrant Mucin expression, altered properties of mucus or epithelial inflammatory processes involving Mucins

30. The method of any one of Claims 26-28, wherein said disease condition is selected from the group consisting of colorectal cancer (CRC), cystic fibrosis (CF), inflammatory bowel disease (IBD), breast cancer (BC), Crohn's disease, ulcerative colitis, asthma and chronic bronchitis.

31. The method of Claim 30, wherein said disease condition is selected from the group consisting of colorectal cancer (CRC), cystic fibrosis (CF), inflammatory bowel disease (IBD) and breast cancer (BC).

32. The method of any one of Claims 26-31, wherein the mammal is a human.