# Patent

## Title
MUC17 encoding nucleic acid sequences, polypeptides, antibodies and methods of use thereof

## Abstract

Disclosed herein are human MUC17-encoding nucleotide sequences, proteins, antibodies, and methods for use thereof.

## Background
GOVERNMENT RIGHTS
Pursuant to 35 U.S.C. §202(c), it is acknowledged that the U.S. Government has certain rights in the invention described herein, which was made in part with funds from the National Institutes of Health, Grant Number: 5 RO1-CA078590-06.


FIELD OF THE INVENTION
This invention relates to the fields of molecular biology and oncology. Specifically, the invention provides MUC17 encoding nucleic acid sequences, polypeptides, antibodies, and methods of use thereof.
BACKGROUND OF THE INVENTION
Several publications and patents are cited in this application in order to more fully describe the state of the art to which this invention pertains. The disclosure of each of these citations is incorporated by reference herein.
Adenocarcinoma of pancreatic ducts is the fifth leading cause of cancer-related deaths in the United States (1;2). The survival time for patients diagnosed with pancreatic cancer ranges from three to six months on average, with a 5% chance of five-year survival. The highest cure rate occurs if the tumor is truly localized to the pancreas; however, this stage of disease accounts for fewer than 20% of cases. For those patients with localized disease and small cancers (<2 centimeters), with no lymph node metastases and no extension beyond the “capsule” of the pancreas, complete surgical resection can yield actuarial 5-year survival rates of 18% to 24% (3;4). Unfortunately, the signs of early stage pancreatic cancer are vague, and often attributed to other problems by both patients and physicians. More specific symptoms tend to develop after the tumor has grown to invade other organs or blocked the bile ducts. Patients are usually diagnosed at an advanced stage, with a high incidence of associated metastases, which spread throughout the body.
There are no tumor-specific markers for pancreatic cancer; markers such as serum CA19-9 have low specificity (5). 65% of patients with pancreatic cancer will have CA19-9 levels greater than 120 U/L, whereas only 2% of cases of pancreatitis will have levels this high. Indeed, CA-19-9 levels increase with pancreatic cancer (97%) to values greater than 1000 U/L, however most of these cancers will be unresectable. Anti-CA19-9 recognizes a mucin-type glycoprotein sialosyl lewis antigen (6). For over two decades, oligosaccharide structure antigens such as CA19-9, DUPAN2, or CA125 were heavily investigated for the development of serum-based immunoassays for the early detection of cancers. These saccharidic epitopes are carried by high molecular weight glycoproteins called mucins. CA19-9 (7;8) and DUPAN2 (7;9) are present in MUC1 and CA125 is present in MUC16 (10; 11).
Interestingly, both mucin gene expression and the glycosylation pattern of mucins are dysregulated in cancer development and progression. Indeed, a specific mucin expression pattern is usually associated with one type of adenocarcinoma, which is distinct from its normal counterpart. For instance, it has previously been reported that overexpression of the MUC1 gene and aberrant expression of the MUC4 gene is associated with pancreatic cancer development and progression. MUC4 is highly expressed in human pancreatic tumors and pancreatic tumor cell lines, but is minimally or not expressed in normal pancreas or chronic pancreatitis (12–15). MUC4 is expressed by metasplastic ducts and its expression increases with higher grade in Pancreatic intraepithelial neoplasias (PanINs) (16). However, MUC4 is expressed by only 70 to 75% of the pancreatic tumors studied.
Mucins, the main components of the mucus network, are high molecular weight O-glycoproteins expressed and secreted by epithelial cells and in some case by endothelial cells. Their principal function is to protect and lubricate epithelial surfaces, and recent reports demonstrate that mucins and more specifically membrane-bound mucins might play a key role in the initiation and transduction of signals, which trigger apoptosis and/or proliferation. The rMuc4 (rat homologue of human MUC4) forms a ligand-receptor type intramembrane complex with HER2, induces its phosphorylation and triggers survival of cells by repression of apoptosis (17).
Currently, nineteen genes are within the MUC gene family and include: MUC1–2, MUC3, MUC4, MUC5AC, MUC5B, MUC6–13, MUC15–19 (18–22). These mucins can further be grouped in two subfamilies, e.g. secreted mucins and membrane-bound mucins. Secreted mucins are expressed exclusively by specialized epithelial cells, are secreted in the mucus, and demonstrate a restricted expression pattern within the human body. Membrane-bound mucins, composed of MUC1, MUC3, MUC4, MUC12–13, MUC16, and MUC17 often possess EGF-like domains (MUC3, 4, 12, 13, and 17) and appear to share numerous common properties. As compared to the secreted mucins, membrane-bound mucins demonstrate a wide and complex expression pattern. They can be expressed in four distinct forms; 1) membrane-anchored, 2) soluble (proteolytic cleavage of the membrane-bound form), 3) secreted (alternative splice variants), and 4) lacking the tandem repeat array (alternatively spliced variants) (14;23–26). The ratio of one form to another appears to be tissue specific as is association with the physiologic condition, e.g.,(normal or malignant phenotypes) (26;27).
SUMMARY OF THE INVENTION
In accordance with the present invention, methods and compositions for detecting pancreatic cancer are provided. Specifically, two MUC17 encoding nucleic acids are disclosed, as well as methods of detecting pancreatic cancer by detecting elevations in expression levels of the same.
One embodiment of the invention comprises an isolated, enriched, or purified nucleic acid molecule encoding MUC17 or a secreted variant thereof designated as MUC17sec herein. Exemplary nucleic acids encoding these MUC17 proteins have the sequences of SEQ ID NOS 1 and 2 and encode MUC 17 proteins of SEQ ID NOS: 3 and 4 respectively.
Also provided in accordance with the invention are oligonucleotides, including probes and primers, that specifically hybridize with the nucleic acid sequences set forth above.
In a further aspect of the invention, recombinant DNA molecules comprising the nucleic acid molecules set forth above, operably linked to a vector are provided. The invention also encompasses host cells comprising a vector encoding the MUC17 polypeptides of the invention.
One embodiment of the invention comprises an isolated, enriched, or purified MUC17 polypeptide. Preferably, the MUC17 polypeptide is full length or an alternatively spliced secreted variant. Most preferably, a MUC17 polypeptide is the polypeptide encoded by SEQ ID NOS:1 or 2, or is the polypeptide of SEQ ID NO:3 or 4.
In another aspect of the invention, an antibody immunologically specific for a MUC 17 polypeptide is provided. Such antibodies may be monoclonal or polyclonal, and include recombinant, chimerized, humanized, antigen binding fragments of such antibodies, and anti-idiotypic antibodies.
In another aspect of the invention, methods for detecting MUC17 associated molecules in a biological sample are provided. Such molecules can be MUC17 encoding nucleic acids, such as mRNA, DNA, cDNA, or MUC17 encoded polypeptides or fragments thereof. Exemplary methods comprise mRNA analysis, for example by RT-PCR. Immunological methods include for example contacting a sample with a detectably labeled antibody immunologically specific for a MUC17 polypeptide and determining the presence of the polypeptide as a function of the amount of detectably labeled antibody bound by the sample relative to control cells. In a preferred embodiment, these assays may be used to detect MUC17 or the secreted variant thereof. In a most preferred embodiment, assays which detect MUC17 are used to diagnose pancreatic cancer. In an alternative embodiment of the method, MUC 4 and MUC 12 expression levels are also examined as these mucins have previously been associated with the occurrence of pancreatic cancer.
In another aspect of the invention, recombinant organisms, or transgenic organisms which have a new combination of genes or nucleic acid molecules are provided.
In a further aspect of the invention, kits for detection of pancreatic cancer are provided. An exemplary kit comprises a MUC17 protein, polynucleotide, or antibody, which are optionally linked to a detectable label. The kits may also include a pharmaceutically acceptable carrier and/or excipient, a suitable container, and instructions for use.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a pair of gels showing the expression of membrane-bound mucin genes in normal pancreas and pancreatitis tissue samples. Total RNA from two normal pancreatic and eight pancreatitis tissue samples were analyzed by RT-PCR using primers specific for MUC1, 3, 4, 12, 13, 16, and 17. β actin was used as internal control. Only MUC1 and MUC13 were detected in the normal pancreas specimen while MUC1, MUC13, and MUC16 were detected in the pancreatitis tissue samples.
FIG. 2 is a gel showing the expression of membrane-bound mucin genes in sixteen pancreatic adenocarcinoma tissue samples. Total RNAs were prepared using the guanidinium isothiocyanate-cesium chloride ultracentrifugation method and analyzed by RT-PCR. β actin was used as internal control. MUC1, MUC13, and MUC16 were detected respectively in 100, 56, and 95% of the samples. As disclosed previously (28), MUC4 was detected in 93% of the samples. MUC3, MUC12, and MUC17 were expressed in 6, 75, and 87% of the specimens tested.
FIGS. 3A–3D are schematic drawings of the structure of the MUC17 gene and the protein encoded thereby. A) MUC17 is clustered with MUC3 and MUC12 on chromosome 7 in the region q22. MUC17 is oriented centromere to telomere between MUC12 and Serpine 1. B) MUC17 encompasses 13 exons and overlaps 39 kb of genomic DNA. Its first exon is located at 1146 bp from the last exon of MUC12. The black triangle indicates a position in exon 7 where alternative splicing occurs. C) MUC17 RNA is 14221 bp long and codes for a membrane-bound mucin. Its central domain is composed of 64 repeating motifs of 59 amino acid residues rich in serine, threonine, and proline. A 25 amino acid signal peptide is found at the N-terminus. D) An alternative splice event, which excludes exon 7, gives rise to the secreted form of MUC17, MUC17/SEC. MUC17/SEC lacks the unique sequence located upstream of the SEA module, as well as the second EGF-like domain, transmembrane sequence and the cytoplasmic tail. The last 21 residues are specific to MUC17/SEC.
FIG. 4 is a gel showing the results of in vitro transcription and translation of the MUC17 complete coding region (SEQ ID NO: 3).
FIG. 5 is a Southern Blot of genomic DNA from various pancreatic tumor cell lines. After digestion with EcoRI and Pst I, the DNA was fractionated on an 0.8% agarose gel. The blot was probed with a 32P-labeled tandem repeat sequence of MUC 17.
FIGS. 6A–6G show the nucleotide sequence of MUC17-encoding sequence, SEQ ID NO: 1.
FIGS. 7A–7G show the nucleotide sequence of MUC17SEC-encoding sequence, SEQ ID NO: 2.
FIGS. 8A and 8B show the amino acid sequence of MUC17 protein, SEQ ID NO: 3.
FIGS. 9A and 9B show the amino acid sequence of MUC17SEC protein, SEQ ID NO: 4.



DETAILED DESCRIPTION OF THE INVENTION
The present invention relates to the discovery of full-length MUC17-encoding sequence (SEQ ID NO: 1) and a variant MUC17SEC-encoding sequence (SEQ ID NO: 2), which encode the full-length MUC17 protein (SEQ ID NO: 3) and a variant MUC17 secreted protein (SEQ ID NO: 4), respectively. The present invention also relates to antibodies having binding affinity for MUC17 or MUC17SEC protein. As used herein, a “MUC17 protein” or “MUC17 polypeptide” may refer to both the MUC17 protein of SEQ ID NO: 3 and the variant MUC17SEC protein of SEQ ID NO: 4.
The present invention further relates to methods for diagnosing pancreatic caner in patients by detecting the expression levels of MUC17 related molecules which include without limitation MUC17 acids. (e.g. DNA and RNA) and MUC17 proteins or polypeptides. The method optionally includes detecting the expression levels of other mucin genes, such as MUC4 and MUC12.
Also encompassed within the invention are kits for performing the methods described above.
I. Preparation of Human MUC17-Encoding Nucleic Acid Molecules, MUC 17 Proteins, and Antibodies thereto
Nucleic Acid Molecules: Nucleic acid molecules encoding the human MUC17 proteins of the invention may be prepared by two general methods: (1) synthesis from appropriate nucleotide triphosphates, or (2) isolation from biological sources. Both methods utilize protocols well known in the art. The availability of nucleotide sequence information, such as cDNAs having the sequences of SEQ ID NOs: 1 and 2, enables preparation of an isolated nucleic acid molecule of the invention by oligonucleotide synthesis. Synthetic oligonucleotides may be prepared by the phosphoramidite method employed in the Applied Biosystems 38A DNA Synthesizer or similar devices. The resultant construct may be purified according to methods known in the art, such as high performance liquid chromatography (HPLC). Long, double-stranded polynucleotides, such as a DNA molecule of the present invention, must be synthesized in stages, due to the size limitations inherent in current oligonucleotide synthetic methods. Thus, for example, a 14 kb double-stranded molecule may be synthesized as several smaller segments of appropriate complementarity. Complementary segments thus produced may be annealed such that each segment possesses appropriate cohesive termini for attachment of an adjacent segment. Adjacent segments may be ligated by annealing cohesive termini in the presence of DNA ligase to construct an entire 14 kb double-stranded molecule. A synthetic DNA molecule so constructed may then be cloned and amplified in an appropriate vector. Nucleic acid sequences encoding the human MUC17 protein may be isolated from appropriate biological sources using methods known in the art. In a preferred embodiment, a cDNA clone is isolated from a cDNA expression library of human origin. In an alternative embodiment, utilizing the sequence information provided by the cDNA sequence, human genomic clones encoding MUC17 proteins may be isolated. Suitable probes for this purpose are derived from sequences within the MUC17 cDNAs.
Additionally, cDNAs or genomic clones having homology with human MUC17 may be isolated from other species using oligonucleotide probes corresponding to predetermined sequences within the human MUC17 encoding nucleic acids.
In accordance with the present invention, nucleic acids having the appropriate level of sequence homology with the protein coding region of SEQ ID NOs: 1 or 2 may be identified by using hybridization and washing conditions of appropriate stringency. For example, hybridizations may be performed, according to the method of Sambrook et al., Molecular Cloning, Cold Spring Harbor Laboratory (1989), using a hybridization solution comprising: 5×SSC, 5× Denhardt's reagent, 1.0% SDS, 100 μg/ml denatured, fragmented salmon sperm DNA, 0.05% sodium pyrophosphate and up to 50% formamide. Hybridization is carried out at 37–42° C. for at least six hours. Following hybridization, filters are washed as follows: (1) 5 minutes at room temperature in 2×SSC and 1% SDS; (2) 15 minutes at room temperature in 2×SSC and 0.1% SDS; (3) 30 minutes-1 hour at 37° C. in 1×SSC and 1% SDS; (4) 2 hours at 42–65° C. in 1×SSC and 1% SDS, changing the solution every 30 minutes.
One common formula for calculating the stringency conditions required to achieve hybridization between nucleic acid molecules of a specified sequence homology (Sambrook et al., 1989) is as follows:

Tm=81.5° C.+16.6 Log [Na+]+0.41(% G+C)−0.63 (% formamide)−600/#bp in duplex

As an illustration of the above formula, using [Na+]=[0.368] and 50% formamide, with GC content of 42% and an average probe size of 200 bases, the Tm is 57° C. The Tm of a DNA duplex decreases by 1–1.5° C. with every 1% decrease in homology. Thus, targets with greater than about 75% sequence identity would be observed using a hybridization temperature of 42° C.
The stringency of the hybridization and wash depend primarily on the salt concentration and temperature of the solutions. In general, to maximize the rate of annealing of the probe with its target, the hybridization is usually carried out at salt and temperature conditions that are 20–25° C. below the calculated Tm of the hybrid. Wash conditions should be as stringent as possible for the degree of identity of the probe for the target. In general, wash conditions are selected to be approximately 12–20° C. below the Tm of the hybrid. In regards to the nucleic acids of the current invention, a moderate stringency hybridization is defined as hybridization in 6×SSC, 5× Denhardt's solution, 0.5% SDS and 100 μg/ml denatured salmon sperm DNA at 42° C., and washed in 2×SSC and 0.5% SDS at 55° C. for 15 minutes. A high stringency hybridization is defined as hybridization in 6×SSC, 5× Denhardt's solution, 0.5% SDS and 100 μg/ml denatured salmon sperm DNA at 42° C., and washed in 1×SSC and 0.5% SDS at 65° C. for 15 minutes. A very high stringency hybridization is defined as hybridization in 6×SSC, 5× Denhardt's solution, 0.5% SDS and 100 μg/ml denatured salmon sperm DNA at 42° C., and washed in 0.1×SSC and 0.5% SDS at 65° C. for 15 minutes.
Nucleic acids of the present invention may be maintained as DNA in any convenient cloning vector. In a preferred embodiment, clones are maintained in a plasmid cloning/expression vector, such as pBluescript (Stratagene, La Jolla, Calif.), which is propagated in a suitable E. coli host cell.
MUC17-encoding nucleic acid molecules of the invention include cDNA, genomic DNA, RNA, and fragments thereof which may be single- or double-stranded. Thus, this invention provides oligonucleotides having sequences capable of hybridizing with at least one sequence of a nucleic acid molecule of the present invention, such as selected segments of the cDNA having SEQ ID NOs: 1 or 2. As mentioned previously, such oligonucleotides are useful as probes for detecting or isolating MUC17 genes.
Antisense nucleic acid molecules may be targeted to translation initiation sites and/or splice sites to inhibit the expression of the MUC17 gene or production of the MUC17 protein of the invention. Such antisense molecules are typically between 15 and 30 nucleotides in length and often span the translational start site of MUC17 encoding mRNA molecules.
Alternatively, antisense constructs may be generated which contain the entire MUC17 cDNAs in reverse orientation. Such antisense constructs are endompassed by the present invention.
It will be appreciated by persons skilled in the art that variants (e.g., allelic variants) of MUC17 sequences exist in the human population, and must be taken into account when designing and/or utilizing oligonucleotides of the invention. Accordingly, it is within the scope of the present invention to encompass such variants, with respect to the MUC17 sequences disclosed herein or the oligonucleotides targeted to specific locations on the respective genes or RNA transcripts. Accordingly, the term “natural allelic variants” is used herein to refer to various specific nucleotide sequences of the invention and variants thereof that would occur in a human population. The usage of different wobble codons and genetic polymorphisms which give rise to conservative or neutral amino acid substitutions in the encoded protein are examples of such variants. Additionally, the term “substantially complementary” refers to oligonucleotide sequences that may not be perfectly matched to a target sequence, but such mismatches do not materially affect the ability of the oligonucleotide to hybridize with its target sequence under the conditions described.
Proteins: Full-length human MUC17 protein (SEQ ID NO: 3) and its variant MUC17SEC protein (SEQ ID NO: 4) of the present invention may be prepared in a variety of ways, according to known methods. The protein may be purified from appropriate sources, e.g., transformed bacterial or animal cultured cells or tissues, by immunoaffinity purification. However, this is not a preferred method due to the low amount of protein likely to be present in a given cell type at any time. The availability of nucleic acid molecules encoding MUC17 and MUC17SEC proteins enables production of the protein using in vitro expression methods known in the art. For example, a cDNA or gene may be cloned into an appropriate in vitro transcription vector, such as pSP64 or pSP65 for in vitro transcription, followed by cell-free translation in a suitable cell-free translation system, such as wheat germ or rabbit reticulocyte lysates. In vitro transcription and translation systems are commercially available, e.g., from Promega Biotech, Madison, Wis. or Gibco-BRL, Gaithersburg, Md.
Alternatively, according to a preferred embodiment, larger quantities of MUC17 or MUC17SEC proteins may be produced by expression in a suitable prokaryotic or eukaryotic system. For example, part or all of a DNA molecule, such as a cDNA having SEQ ID NOs: 1 or 2 may be inserted into a plasmid vector adapted for expression in a bacterial cell, such as E. coli. Such vectors comprise the regulatory elements necessary for expression of the DNA in the host cell positioned in such a manner as to permit expression of the DNA in the host cell. Such regulatory elements required for expression include promoter sequences, transcription initiation sequences and, optionally, enhancer sequences.
The human MUC17 protein (SEQ ID NO: 3) or its variant form (SEQ ID NO: 4) produced by gene expression in a recombinant procaryotic or eukaryotic system may be purified according to methods known in the art. In a preferred embodiment, a commercially available expression/secretion system can be used, whereby the recombinant protein is expressed and thereafter secreted from the host cell, and readily purified from the surrounding medium. If expression/secretion vectors are not used, an alternative approach involves purifying the recombinant protein by affinity separation, such as by immunological interaction with antibodies that bind specifically to the recombinant protein or nickel columns for isolation of recombinant proteins tagged with 6–8 histidine residues at their N-terminus or C-terminus. Alternative tags may comprise the FLAG epitope or the hemagglutinin epitope. Such methods are commonly used by skilled practitioners.
The human MUC17 protein and its variant, prepared by the aforementioned methods, may be analyzed according to standard procedures. For example, such proteins may be subjected to amino acid sequence analysis, according to known methods.
Antibodies: The present invention also provides antibodies capable of immunospecifically binding to proteins of the invention. Polyclonal antibodies directed toward human MUC17 proteins may be prepared according to standard methods. In a preferred embodiment, monoclonal antibodies are prepared, which react immunospecifically with the various epitopes of the MUC17 proteins described herein. Monoclonal antibodies may be prepared according to general methods of Köhler and Milstein, following standard protocols. Polyclonal or monoclonal antibodies that immunospecifically interact with MUC17 proteins can be utilized for identifying and purifying such proteins. For example, antibodies may be utilized for affinity separation of proteins with which they immunospecifically interact. Antibodies may also be used to immunoprecipitate proteins from a sample containing a mixture of proteins and other biological molecules. Other uses of anti-MUC17 antibodies are described below.
II. Uses of MUC17-Encoding Nucleic Acids, MUC17 Proteins and Antibodies thereto
In accordance with the present invention, MUC4, MUC12, and MUC17 are specifically up-regulated in pancreatic adenocarcinoma specimens (FIGS. 1 and 2). Thus, the MUC17 nucleic acids, proteins, and anti-MUC17 antibodies may be used for diagnosing pancreatic cancer in patients.
Additionally, the methods for diagnosing pancreatic cancer may further comprise assessing MUC4 and/or MUC12 expression levels in the patients. The nucleic acid sequences encoding human MUC4 and MUC12 are available in GenBank. MUC 4 Accession numbers are AJ276359, AJ100901 and AJ000281. The MUC12 Accession number is AF147790.
MUC17-Encoding Nucleic Acids: MUC17-encoding nucleic acids may be used for a variety of purposes in accordance with the present invention. MUC17-encoding DNA, RNA, or fragments thereof may be used as probes to detect the presence of and/or expression of genes encoding MUC17 proteins. Methods in which MUC17-encoding nucleic acids may be utilized as probes for such assays include, but are not limited to: (1) in situ hybridization; (2) Southern hybridization (3) northern hybridization; and (4) assorted amplification reactions such as polymerase chain reactions (PCR). Thus, MUC17-encoding nucleic acids of the present invention may be used for detecting up-regulation of MUC17 genes in patients and thereby determining the presence of pancreatic carcinoma in the patients.
Further, the MUC17-encoding nucleic acids of the invention may also be utilized as probes to identify related genes from other animal species. As is well known in the art, hybridization stringencies may be adjusted to allow hybridization of nucleic acid probes with complementary sequences of varying degrees of homology.
Thus, MUC17-encoding nucleic acids may be used to advantage to identify and characterize other genes of varying degrees of relation to the MUC17 genes of the invention thereby enabling further identification of genes whose up-regulation is associated with pancreatic adenocarcinomas. Additionally, the nucleic acids of the invention may be used to identify genes encoding proteins that interact with MUC17 proteins (e.g., by the “interaction trap” technique).
Nucleic acid molecules, or fragments thereof, encoding MUC17 genes may also be utilized to control the production of MUC17 proteins in target cells. As mentioned above, antisense oligonucleotides corresponding to essential processing sites in MUC17-encoding mRNA molecules may be utilized to inhibit MUC17 protein production in targeted cells. Alterations in the physiological amount of MUC17 proteins may dramatically affect the activity of other protein factors involved in the progression of pancreatic carcinoma.
The MUC17 nucleic acids of the invention may be introduced into host cells. In a preferred embodiment, mammalian cell lines are provided which comprise a MUC17-encoding nucleic acid or a variant thereof. Host cells contemplated for use include, but are not limited to NIH3T3, CHO, HELA, yeast, bacteria, insect and plant cells. The MUC17 encoding nucleic acids may be operably linked to appropriate regulatory expression elements suitable for the particular host cell to be utilized. Methods for introducing nucleic acids into host cells are well known in the art. Such methods include, but are not limited to, transfection, transformation, calcium phosphate precipitation, electroporation and lipofection.
The host cells described above may be used as screening tools to identify compounds that modulate MUC17 expression and/or activity. Modulation of MUC17 expression and/or activity may be assessed by measuring alterations in MUC17 mRNA or protein levels in the presence of the test compound.
The availability of MUC17 encoding nucleic acids enables the production of strains of laboratory mice carrying part or all of the MUC17 gene or mutated sequences thereof, in single or amplified copies. Such mice may provide an in vivo model for cancer, and may be particularly useful in studying pancreatic cancer. Alternatively, the human MUC17 nucleic acid sequence information provided herein enables the cloning of the murine homolog for use in the production of knockout mice in which the endogenous gene encoding MUC17 has been specifically inactivated. Methods of introducing transgenes and knockouts in laboratory mice are known to those of skill in the art. Three common methods include: 1) integration of retroviral vectors encoding the foreign gene of interest into an early embryo; 2) injection of DNA into the pronucleus of a newly fertilized egg; and 3) the incorporation of genetically manipulated embryonic stem cells into an early embryo. Production of the transgenic and knockout mice described above will facilitate the molecular elucidation of the role MUC17 proteins play in differentiation and tumorigenesis.
The alterations to the MUC17 gene envisioned herein include modifications, deletions, and substitutions. Modifications and deletions render the naturally occurring gene nonfunctional, producing a “knock out” animal. Substitutions of the naturally occurring gene for a gene from a second species results in an animal that produces a MUC17 gene from the second species. Substitution of the naturally occurring gene for a gene having a mutation results in an animal with a mutated MUC17 protein. A transgenic mouse carrying the human MUC17 gene is generated by direct replacement of the mouse MUC17 gene with the human gene. These transgenic animals are valuable for use in vivo assays for elucidation of other medical disorders associated with cellular activities modulated by MUC17 genes. A transgenic animal carrying a “knock out” of a MUC17-encoding nucleic acid is useful for the establishment of a nonhuman model for pancreatic cancer involving MUC17 regulation.
As a means to define the role that MUC17 plays in mammalian systems, mice can be generated that cannot make MUC17 proteins because of a targeted mutational disruption of a MUC17 gene.
The term “animal” as used in this section includes all vertebrate animals, except humans. It also includes an individual animal in all stages of development, including embryonic and fetal stages. A “transgenic animal” is any animal containing one or more cells bearing genetic information altered or received, directly or indirectly, by deliberate genetic manipulation at the subcellular level, such as by targeted recombination or microinjection or infection with recombinant virus. The term “transgenic animal” is not meant to encompass classical cross-breeding or in vitro fertilization, but rather is meant to encompass animals in which one or more cells are altered by or receive a recombinant DNA molecule. This molecule may be specifically targeted to a defined genetic locus, be randomly integrated within a chromosome, or it may be extrachromosomally replicating DNA. The term “germ cell line transgenic animal” refers to a transgenic animal in which the genetic alteration or genetic information was introduced into a germ line cell, thereby conferring the ability to transfer the genetic information to offspring. If such offspring in fact, possess some or all of that alteration or genetic information, then they, too, are transgenic animals.
The alteration or genetic information may be foreign to the species of animal to which the recipient belongs, or foreign only to the particular individual recipient, or may be genetic information already possessed by the recipient. In the last case, the altered or introduced gene may be expressed differently than the native gene.
The altered MUC17 gene generally should not fully encode the same MUC17 protein native to the host animal and its expression product should be altered to a minor or great degree, or absent altogether. However, it is conceivable that a more modestly modified MUC17 gene will fall within the scope of the present invention if it is a specific alteration.
The DNA used for altering a target gene may be obtained by a wide variety of techniques that include, but are not limited to, isolation from genomic sources, preparation of cDNAs from isolated mRNA templates, direct synthesis, or a combination thereof. A preferred type of target cell for transgene introduction is the embryonal stem (ES) cell. ES cells may be obtained from pre-implantation embryos cultured in vitro. Transgenes can be efficiently introduced into the ES cells by standard techniques such as DNA transfection or by retrovirus-mediated transduction. The resultant transformed ES cells can thereafter be combined with blastocysts from a non-human animal. The introduced ES cells thereafter colonize the embryo and contribute to the germ line of the resulting chimeric animal.
One approach to the problem of determining the contributions of individual genes and their expression products is to use isolated MUC17 genes to selectively inactivate the wild-type gene in totipotent ES cells (such as those described above) and then generate transgenic mice. The use of gene-targeted ES cells in the generation of gene-targeted transgenic mice is known in the art.
Techniques are available to inactivate or alter any genetic region to a mutation desired by using targeted homologous recombination to insert specific changes into chromosomal alleles. However, in comparison with homologous extrachromosomal recombination, which occurs at a frequency approaching 100%, homologous plasmid-chromosome recombination was originally reported to only be detected at frequencies between 10−6 and 10−3. Nonhomologous plasmid-chromosome interactions are more frequent occurring at levels 105-fold to 102-fold greater than comparable homologous insertion.
To overcome this low proportion of targeted recombination in murine ES cells, various strategies have been developed to detect or select rare homologous recombinants. One approach for detecting homologous alteration events uses the polymerase chain reaction (PCR) to screen pools of transformant cells for homologous insertion, followed by screening of individual clones. Alternatively, a positive genetic selection approach has been developed in which a marker gene is constructed which will only be active if homologous insertion occurs, allowing these recombinants to be selected directly. One of the most powerful approaches developed for selecting homologous recombinants is the positive-negative selection (PNS) method developed for genes for which no direct selection of the alteration exists. The PNS method is more efficient for targeting genes which are not expressed at high levels because the marker gene has its own promoter. Non-homologous recombinants are selected against by using the Herpes Simplex virus thymidine kinase (HSV-TK) gene and selecting against its nonhomologous insertion with effective herpes drugs such as gancyclovir (GANC) or (1-(2-deoxy-2-fluoro-B-D arabinofluranosyl)-5-iodouracil, (FIAU). By this counter selection, the number of homologous recombinants in the surviving transformants can be increased.
As used herein, a “targeted gene” or “knock-out” is a DNA sequence introduced into the germline or a non-human animal by way of human intervention, including but not limited to, the methods described herein. The targeted genes of the invention include DNA sequences which are designed to specifically alter cognate endogenous alleles.
Methods of use for the transgenic mice of the invention are also provided herein. Knockout mice of the invention can be injected with tumor cells or treated with carcinogens to generate carcinomas. Such mice provide a biological system for assessing the role played by a MUC17 gene of the invention. Accordingly, therapeutic agents which inhibit the expression and/or action of MUC17 proteins may be screened in studies using MUC17 knock out mice.
As described above, MUC17-encoding nucleic acids are also used to advantage to produce large quantities of substantially pure MUC17 proteins, or selected portions thereof.
MUC17 Protein and Antibodies: Purified MUC17 protein, or fragments thereof, may be used to produce polyclonal or monoclonal antibodies which also may serve as sensitive detection reagents for the presence and accumulation of MUC17 protein (or complexes containing MUC17 protein) in mammalian cells. Recombinant techniques enable expression of fusion proteins containing part or all of MUC17 protein. The full length protein or fragments of the protein may be used to advantage to generate an array of monoclonal antibodies specific for various epitopes of MUC17 protein, thereby providing even greater sensitivity for detection of MUC17 protein in cells.
Polyclonal or monoclonal antibodies immunologically specific for MUC17 protein may be used in a variety of assays designed to detect and quantitate the protein. Such assays include, but are not limited to: (1) flow cytometric analysis; (2) immunochemical detection/localization of MUC17 protein in tumor cells or cells in various stages of differentiation; and (3) immunoblot analysis (e.g., dot blot, Western blot) of extracts from various cells. Additionally, as described above, anti-MUC17 antibodies can be used for purification of MUC17 protein and any associated subunits (e.g., affinity column purification, immunoprecipitation).
From the foregoing discussion, it can be seen that MUC17-encoding nucleic acids, MUC17 expressing vectors, MUC17 protein and anti-MUC17 antibodies of the invention can be used to detect MUC17 gene expression and alter MUC17 protein accumulation.
Methods of Use for the Compositions of the Invention and Kits for Performing the Disclosed Methods:
Exemplary approaches for detecting MUC17 nucleic acids or polypeptides/proteins include:
a) comparing the amount of MUC17 mRNAs in the sample from a patient suspecting having pancreatic cancer with that from a healthy subject without pancreatic cancer; or
b) comparing the amount of MUC17 proteins in the sample from a patient suspecting having pancreatic cancer with that from a healthy subject without pancreatic cancer; or
c) using a specific binding member capable of binding to a MUC17 nucleic acid sequence or the polypeptide encoded by it, the specific binding member comprising nucleic acid hybridizable with the MUC17 sequence, or substances comprising an antibody domain with specificity for MUC17 nucleic acid sequence or the polypeptide encoded by it, the specific binding member being labelled so that binding of the specific binding member to its binding partner is detectable and/or quantifiable.
A “specific binding pair” comprises a specific binding member (sbm) and a binding partner (bp) which have a particular specificity for each other and which in normal conditions bind to each other in preference to other molecules. Examples of specific binding pairs are antigens and antibodies, ligands and receptors and complementary nucleotide sequences. The skilled person is aware of many other examples and they do not need to be listed here. Further, the term “specific binding pair” is also applicable where either or both of the specific binding member and the binding partner comprise a part of a large molecule. In embodiments in which the specific binding pair comprise nucleic acid sequences, they will be of a length to hybridize to each other under conditions of the assay, preferably greater than 10 nucleotides long, more preferably greater than 15 or 20 nucleotides long.
In most embodiments for screening for cancer, the MUC17 nucleic acid in the sample will initially be amplified, e.g. using RT-PCR, to increase the amount of the analyte as compared to other sequences present in the sample. This allows the target sequences to be detected with a high degree of sensitivity if they are present in the sample. This initial step may be avoided by using highly sensitive array techniques that are becoming increasingly important in the art.
In still further embodiments, the present invention concerns immunodetection methods for binding, purifying, removing, quantifying or otherwise generally detecting biological components. The encoded proteins or peptides of the present invention may be employed to detect antibodies having reactivity therewith, or, alternatively, antibodies prepared in accordance with the present invention, may be employed to detect the encoded proteins or peptides.
In terms of antigen detection, the biological sample analyzed may be any sample that is suspected of containing the MUC17 antigen, such as a pancreas or lymph node tissue section or specimen, a homogenized tissue extract, an isolated cell, a cell membrane preparation, separated or purified forms of any of the above protein-containing compositions, or even any biological fluid that comes into contact with pancreatic tissues, including blood and lymphatic fluid.
Contacting the chosen biological sample with the antibody under conditions effective and for a period of time sufficient to allow the formation of immune complexes (primary immune complexes) is generally a matter of simply adding the composition to the sample and incubating the mixture for a period of time long enough for the antibodies to form immune complexes with, i.e., to bind to, any MUC17 antigens present. After this time, the sample-antibody composition, such as a tissue section, ELISA plate, dot blot or Western blot, will generally be washed to remove any non-specifically bound antibody species, allowing only those antibodies specifically bound within the primary immune complexes to be detected.
In general, the detection of immunocomplex formation is well known in the art and may be achieved through the application of numerous approaches. These methods are generally based upon the detection of a label or marker, such as any radioactive, fluorescent, biological or enzymatic tags or labels of standard use in the art. U.S. patents concerning the use of such labels include U.S. Pat. Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149 and 4,366,241, each incorporated herein by reference. Of course, one may find additional advantages through the use of a secondary binding ligand such as a second antibody or a biotin/avidin ligand binding arrangement, as is known in the art. The immunodetection methods of the present invention have evident utility in the diagnosis of pancreatic cancer.
In the clinical diagnosis or monitoring of patients with pancreatic cancer, the detection of MUC17 antigen, or an increase in the levels of such an antigen, in comparison to the levels in a corresponding biological sample from a normal subject is indicative of a patient with pancreatic cancer. The basis for such diagnostic methods lies, in part, with the finding that the MUC17 nucleic acid identified in the present invention is overexpressed in pancreatic cancer tissue samples (see Examples below). By extension, it may be inferred that this nucleic acid produces elevated levels of encoded MUC17 proteins which may also be used as pancreatic cancer markers.
As mentioned previously, cell lines expressing the MUC17-encoding nucleic acids or variants thereof may be used in screening methods to identify agents which modulate MUC17 expression and/or function.
In one broad aspect, the present invention encompasses kits for use in detecting expression of MUC17 in pancreatic tissues. Such a kit may comprise one or more pairs of primers for amplifying nucleic acids corresponding to the MUC17 gene. The kit may further comprise samples of total mRNA derived from tissue of various physiological states, such as normal, early stage and metastatically progressive tumor, for example, to be used as controls. The kit may also comprise buffers, nucleotide bases, and other compositions to be used in hybridization and/or amplification reactions. Each solution or composition may be contained in a vial or bottle and all vials held in close confinement in a box for commercial sale. Another embodiment of the present invention encompasses a kit for use in detecting pancreatic cancer cells in a biological sample comprising oligonucleotide probes effective to bind with high affinity to MUC17 mRNA in a Northern blot assay and containers for each of these probes. In a further embodiment, the invention encompasses a kit for use in detecting MUC17 proteins in pancreatic cancer cells comprising antibodies specific for MUC17 proteins encoded by the MUC17 nucleic acids of the present invention.
Further details regarding the practice of this invention are set forth in the following examples, which are provided for illustrative purposes only and are in no way intended to limit the invention. The following materials and methods are provided to facilitate the practice of the present invention.
Tissue specimens and cell lines—A total of 24 pancreatic adenocarcinomas, 10 pancreatitis tissue samples (all obtained at the time of primary surgery from various patients) and 2 normal pancreatic tissue samples (obtained from previously healthy organ donors) were used in this study. Samples were collected under the protocol approved by the Institutional Review Board at the University of Nebraska Medical Center, Omaha, Nebr., and the Department of Visceral and Transplantation Surgery, University of Bern, Bern, Switzerland. Informed consent was obtained from all subjects. Tissue specimens were frozen in liquid nitrogen and stored at −80° C. until they were processed for RNA extraction.
RNA isolation and reverse transcription RT-PCR analysis—Total RNA was isolated from tissue samples and cell lines by the guanidinium isothiocyanate-cesium chloride ultracentrifugation method (28). Two micrograms of RNA were reverse transcribed using the SuperScriptTMII RNase Reverse Transcriptase system (Invitrogen, USA) Samples were subjected to PCR amplification using the parameters and primers described previously (12;29). Additional primers were: MUC12 (forward GCACATGTCAGCTGCAACGCA; SEQ ID NO: 5, reverse GGCTCTGTGTTTGCAGCTCTC; SEQ ID NO: 6), MUC13 (forward AACTGCTAGCACCACAGCAA; SEQ ID NO: 7, reverse CTCAGTCACAGTCTTCTCATT: SEQ ID NO: 8), MUC16 (forward CAGTCAACTACATGACACATT; SEQ ID NO: 9, reverse ACTCTGTCTACTCTCCGAGCC; SEQ ID NO: 10), MUC17 (forward GACCAGAAGCCATACTGCATC; SEQ ID NO: 11, reverse CTCCTCACTCCCAGACTTCTC; SEQ ID NO: 12). β-actin was used as an internal control. PCR products were electrophoretically resolved on 1% agarose gels stained with ethidium bromide. Photographs were taken under UV light, using the GelExpert software system (Nucleotech, USA). DNA sequencing and comparison with previously published sequences from the GenBank database confirmed the authenticity of PCR products.
5′ Rapid amplification of cDNA ends (RACE procedure.—The 5′ RACE kit (RACE) was used to synthesize first-strand cDNA species from total AsPC1 cell line RNA (2 μg) with specific MUC17 primer (RACE 171: GTGATAGCCTCTGAACTGGCC; SEQ ID NO: 13). Terminal transferase was used to add a poly (dA) tail to the 3′ end of the cDNA. RACE-PCR experiments were performed in 50 μl reaction volumes containing 5 μl of 10× buffer (100 mM Tris/HCl/15 mM MgCl2/500 mM KCl, pH 8.3), 5 μl of 10 mM deoxynucleoside triphosphates, 5 μl of poly(dA)-tailed cDNA, 0.2 μM of each primers (MUC17 specific RACE 172: CATGGTGCTGGCAGGCATACT; SEQ ID NO: 14, and the oligo(dT)-anchor primer provide by the supplier), and 2 units of Taq DNA polymerase (Fermentase). The mixture was denatured at 94° C. for 2 min followed by 30 cycles at 94° C. for 30 s, 60° C. for 1 min and additionally 72° C. for 2 min. The elongation step was extended for an additional 15 min period. A 1 μl amplification product was further amplified by a second PCR reaction with a nested specific primer of MUC17 (RACE 173: GTAGGAGATGAACTTGCCTGA; SEQ ID NO: 15) and the PCR anchor primer (Provided by the supplier Roche). The thermal cycling protocol used was the same as for the primary RACE amplification step. PCR products were electrophoretically resolved on 1% agarose gels stained with ethidium bromide. Photographs were taken under UV light, using the GelExpert software system (Nucleotech, USA). Amplification products were excised and purified with QIAquick® Gel Extraction Kit (QIAgen), cloned into pCR2.1 vector (Invitrogen), and finally sequenced.
Expand long PCR—To identify potential MUC17 splice variants in the 3′-extremity, an RT-PCR strategy was performed, using the ExpandTM Long PCR System (ROCHE) with sense primer CTGTGCCAAGAACCACAACAT; SEQ ID NO: 16 and antisense primer CTCCTCACTCCCAGACTTCTC; SEQ ID NO: 17. Expand long PCR experiments were performed in 50 μl reaction volumes containing 5 μl of AsPC1 cDNA, 5 μl of 10× buffer 3, 2.5 μl of 40 mM deoxynucleoside triphosphates, 0.2 μM of each primer, 0.75 mM MgCl2, and 2.5 units of polymerase mixture (ROCHE). The mixture was denatured at 94° C. for 2 min followed by 30 cycles at 94° C. for 30 s, 60° C. for 1 min and additionally 68° C. for 4 min with elongation time for the last 20 cycles extended 40 s for each cycle. The elongation step was extended for an additional 30 min period. Amplification products were directly cloned into pCR2.1 vector (Invitrogen) and positive clones were further processed for sequencing.
Transcription and translation assay in vitro—An amplification product generated using forward primer GCCAGCTCCTCTGGGGTGAC; SEQ ID NO: 18 and reverse primer RACE 171 (described previously) was subcloned in pCR2.1 under the control to the T7 promoter. The cDNA, coding for a peptide with a predicted size of 36 kDa, comprises the putative Kozak sequence followed by an ATG as well as the 25-residue N-terminal signal sequence. Transcription and translation experiments were performed with the TnT® Quick Coupled Transcription/Translation System (Promega) in accordance with the manufacturer's instructions. The amino acid mixture lacking methionine, supplemented with [35S] methionine, was used. Translation products were analyzed by SDS/PAGE.
Southern blot analysis—Genomic DNA from the human pancreatic tumor cell lines such as Pancl, CD18/HPAF, BxPC3, AsPC1, Capan1, and SW1990 were digested with EcoRI and HindIII restriction endonucleases. Digested products were resolved by electrophoresis in 0.8% agarose gels and transferred to nylon membranes. The blot was hybridized with MUC17 tandem repeat probe. See FIG. 5. The probe was prepared by PCR amplification using MUC17 TR forward primer: GATATGAGCACACCTCTGACC; (SEQ ID NO: 19) and MUC17 TR reverse primer: ATGTTGTGGTTCTTGGCACAG; (SEQ ID NO: 20). A 3-kb amplification product was obtained, subcloned in pCR2.1, and sequences. The corresponding insert was radio labeled using the Random Primers DNA Labeling System (Invitrogen) and [32p]dCTP (ICN).
RESULTS
Pancreatic Expression Pattern of the Membrane-Bound Mucins in Inflammatory and Tumoral Physiologic Conditions Dysregulation of mucins is a frequent occurrence in malignancies of epithelial origin. MUC4 (12;16) has previously been identified as a specific marker for pancreatic cancer and has been proposed as a target for the development of cancer therapy as well as early diagnosis. However, 25% of pancreatic adenocarcinoma tumors studied were negative for MUC4 expression and thus other markers are required to accurately diagnose this type of cancer. To improve the sensitivity of detection and develop an early diagnostic able to screen a wide range of patients, a multi-marker screening method has been developed.
The expression of MUC1, MUC3, MUC4, MUC12, MUC13, MUC16, and MUC17 was studied in a panel of 2 normal pancreas samples, 8 pancreatitis samples, and 16 pancreatic adenocarcinoma samples. As shown in FIG. 1 and FIG. 2, results from RT-PCR analysis revealed an alteration in the expression pattern of the membrane-bound mucins, as tissue progressed from normal to malignant. Indeed, only MUC1 and MUC13 were detected in normal pancreas. Their level of expression was low, at the limit of detection for MUC13. Seven out of 8 pancreatitis specimens expressed MUC1 and MUC13 at a higher level than that observed in the normal pancreas. In addition to MUC1 and MUC13, MUC16 was also detected in 7 out 8 of the pancreatitis tissues. The tissue sample negative for MUC16 expression was also negative for MUC1 and MUC13. As expected, relatively high levels of MUC1 and MUC4 transcripts were detected in 100% and 93%, respectively, of the pancreatic adenocarcinoma specimens tested (FIG. 2). Fifteen out of the 16 samples examined were positive for MUC4 expression, although 3 were at the limit of detection. Surprisingly, MUC13 was detected in only 56% of the tumors tested with a level of expression in the positive samples comparable to that observed in the pancreatitis samples. MUC16, which was slightly expressed in pancreatitis, presented a very high level of expression in 95% of the tumor samples examined. Regarding the mucins clustered on chromosome 7q22, MUC3, MUC12, and MUC17 were expressed at 6%, 75%, and 87%, respectively, in the tumor samples. These results indicate that in addition to MUC4, MUC12 and MUC17 up-regulation is associated with the occurrence of pancreatic cancer.
Identification of the Full Length Sequence of MUC17 MUC17 was identified by computational analysis by Gum et al. (22) who employed a 59 amino acid residue peptide believed at that time to be part of MUC3. The authors were able to demonstrate that this sequence belonged to a new mucin called MUC17 and was clustered on chromosome 7q22 with MUC3 and MUC12. Using RT-PCR techniques, Gum et al cloned the carboxy-terminal sequence of MUC17. With this sequence (accession number AF430017), the human genome resources database from the National Center of Biotechnology information server and the human genome project (DOE Joint Genome Institute Human Genome Project) were screened to precisely localize the MUC17 coding sequence to chromosome 7 in the region q22.1, oriented from centromere to telomere, between the MUC12 gene and the serine proteinase inhibitor SERPINE1. To extend MUC17 sequence in the 5′ end, the 177 bp motif of repetition that characterized the tandem repeat array of MUC17 was positioned in a way to extend the upstream sequence by walking on the chromosome. MUC17 allele in the data base (BAC RP11-395B7 with accession number AC105443) showed 64 repetitions of this motif of 177 bp. Up to 600 bp of degenerated repetitive sequence were located at the 5′-extremity of 177 bp array domain. Three antisense primers were chosen in this degenerate sequence and used to perform a 5′-RACE-PCR on the MUC17 highly expressing pancreatic adenocarcinoma cell line AsPC1. Several amplification products were detected with a size varying from 200 to 800 bp for the first PCR, and from 200 to 700 bp after nested PCR. Products from the nested PCR were cloned and the largest cDNA fragment of 653 bp was sequenced. Its 3′-end was overlapping the 5′-extremity of degenerated repetition located upstream of the 64 motif of 177 bp. Comparing the 5′-end of the RACE-PCR product with the sequence of the BAC RP11-395B7, two new exons were identified. The compiled nucleotide sequences of the RACE-PCR clone, with the 177 bp tandem repeat of the BAC RP11-395B7, and with the sequence identified and characterized by Gum et al (AF430017), allowed us to establish the complete sequence of MUC17 (FIG. 3).
Genomic DNA from pancreatic adenocarcinoma cell lines was digested with HindIII and EcoRI endonuclease enzymes. One HindIII site is located at 5434 bp upstream of the tandem repeat array and one EcoRI site is located at 1128 bp downstream from the repetitive sequence. Digestion using these two enzymes of the BAC RP11-395B7 predicted a fragment of 18.75 kb. Southern blot analysis demonstrated one unique band of 18 kb for all the cell lines investigated with the exception of HPAF and HPAC lines where two close alleles were seen. See FIG. 5. Therefore, in contrast to other mucin genes, MUC17 did not exhibit very high degree of variable number of tandem repeat polymorphisms (VNTR).
MUC17 mRNA is 14221 bp long and overlaps a 39000 bp DNA fragment between MUC12 and SERPINE1 on chromosome 7 in the region q22 (FIG. 3A). MUC17 encompass 13 exons ranging in size from 61 bp to 12185 bp (Table I) whereas intron size ranged from 121 to 10902 bp (FIG. 3B). All the 5′ donor and 3′ acceptor sites were consistent with the consensus gt-ag motifs described for splice sites in Eukaryote genes. The largest exon, E3, is at a central position and is composed of 64 repetitions of a motif of 177 bp, encoding the main O-glycosylated domain of MUC17 which is a hallmark of mucin family members. The N-terminal domain of MUC17 is encoded by 2 exons, the first one, E1, located at 1146 bp from the 3′-extremity of MUC12 last exon. The position of MUC17 first exon was checked by PCR amplification on AsPC1 genomic DNA using a forward primer located in MUC12 last exon and a reverse primer located in MUC17 first exon. The expected amplification product was detected (data not shown). El contains the 5′-UTR as well as the sequence coding for MUC17 signal peptide. A methionine residue at position 54 is contained within the context for initiation of translation, AGAGCTCCGATG, as described by Kozak (30). The Kyte-Doolittle (31) hydropathy plot of the N-terminal extremity of MUC17 show that the initial 25 residues encoded by exon 1 are very hydrophobic. Additionally, the SignalP V1.1 software from the Center for Biological Sequence Analysis predicted the presence of a signal peptide within these 25 amino acid residues with a cleavage site located between position 25 and 26 (AAA-EQ). A schematic representation of MUC17 deduced amino acid sequence is shown in FIG. 3C.







TABLE I





Characteristics of the exon-intron junctions of the MUC17 gene


Capital letters indicate exons and small letters indicate introns.


Positions are defined according to the sequence of MUC17 (XXXXX)




















Protein
Exon


Intron














domain
N°
Size (bp)
5′-Splice donor
Name
Position
Size (bp)

















5′-UTR, leader
1
136
A C A A G G g t g a g t g a c c
1
136–137
10902



sequence


 


amino terminal
2
101
G G A C A G g t a a g g c a a c
2
237–238
379


 


central
3
12185
C A A C A T g t a a g t g a t t
3
12456–12457
4163


 


EGF1
4
132
A C A T A G g t g a g t g c a a
4
12587–12588
729


 


EGF1, SEA
5
129
G A A C A G g t a a g t c t g g
5
12715–12716
351


 


SEA
6
61
G C T A C G g t a a g t g t c t
5′
12775–12776
1101


 


SEA
7
153
G C T C A G g t g a a c t c t g
6
12927–12928
977


 


SEA, EGF2
8
70
C T G A A G g t a g g t g a t a
7
12996–12997
121


 


EGF2
9
160
G T G C C T g t g a g t g c t c
8
13156–13157
1023


 


transmembrane
10
163
G A A A C G g t g a g c g a g c
9
13318–13319
191


sequence


 


cytoplasmic tail
11
99
G C C A A G g t a t t g g c c t
10
13416–13417
2757


 


cytoplasmic tail
12
77
A C A A A G g t a a g a a g g g
11
13492–13493
1730


 


cytoplasmic tail,
13
755


3′-UTR















Protein






domain
Class
3′-Splice acceptor







5′-UTR, leader
3
t c t c t t t c a g A C C T C A




sequence



 



amino terminal
2
t c t t a a a c a g G T T C T G



 



central
2
t t c c a c a g a g G C T T T G



 



EGF1
2
c c c g c c t c a g G G C C A C



 



EGF1, SEA
1
t g c c t t t c a g A T G A A T



 



SEA
3
c c c t c t t c a g T C T T G G



 



SEA
2
t c t t t c a c a g A C A T G A



 



SEA, EGF2
2
c c c c c a c c a g A G G A C T



 



EGF2
3
c c c a t c t c a g C T G C G T



 



transmembrane
3
c c a t c a c t a g G C A A A A



sequence



 



cytoplasmic tail
2
c c t c c a c a a g A T G A T G



 



cytoplasmic tail
1
c t c t t t t c a g A T C C G A



 



cytoplasmic tail,



3′-UTR










The region upstream of the tandem repeat of MUC17 was amplified by PCR on AsPC1 cDNA and subcloned into the PCR2.1 vector (Invitrogen). The positive clones were screen by sequencing and one clone comprising the MUC17 ATG directly downstream the T7 promoter of the PCR2.2 vector was used to perform in vitro transcription and translation using the TnT® Quick Coupled Transcription/translation System (Promega). As negative control, empty vector as well as a vector containing the coding sequence of MUC17 in an antisense orientation was used. FIG. 4 provides the results of these experiments. As expected, a 36 kDa protein was detected using the vector encoding the full length coding sequence for MUC17. No proteins were detected in the negative control samples. As positive control, the β galactosidase gene was used (provide by the supplier Promega). The expected 30 kDa protein is shown on the gel (FIG. 4). Therefore, the ATG located downstream the kozak sequence can initiate translation.
The presence of an alternative splice site in the 3′-extremity of MUC17 was investigated by RT-PCR. For this purpose, a forward primer was chosen in exon 3 (tandem repeat domain) and a reverse primer chosen in the 3′-UTR as described above in materials and methods. Using these primers, an expand long RT-PCR was carried out on AsPC1 cDNA, and the amplification product cloned and screened. Two distinct fragments were identified and fully sequenced. One of the fragments was 100% identical with the previous identified sequence of MUC17 (accession number AF430017). The second fragment revealed the presence of an alternative splice site that resulted in the deletion of exon 7. This alternative splicing event generated a frameshift with a stop codon positioned 66 nucleotides after the intron/exon junction. The resulting protein encoded a secreted form of MUC17, wherein the second EGF domain of the transmembrane domain and cytoplasmic tail were deleted. The last 21 amino acid residue of secreted MUC17 (MUC17SEC) was unique to this spliced form.
Pancreatic adenocarcinoma is the fifth leading cause of cancer in the United States, and the 5-year survival for the patients with this malignancy is less than 5%. Overall, 28,900 people in this country die each year from pancreatic cancer. Its incidence has tripled over the last 40 years. The present invention provides compositions and methods to facilitate detection and diagnosis of this deadly cancer.
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While certain of the preferred embodiments of the present invention have been described and specifically exemplified above, it is not intended that the invention be limited to such embodiments. Various modifications may be made thereto without departing from the scope and spirit of the present invention, as set forth in the following claims.

## Claims

1. An isolated nucleic acid molecule comprising a nucleotide sequence encoding a mucin 17 (MUC17) polypeptide, wherein said MUC17 polypeptide has an amino acid sequence selected from the group consisting of SEQ ID NO: 3 and SEQ ID NO: 4.

2. The isolated nucleic acid molecule of claim 1, wherein said MUC17 polypeptide has the amino acid sequence of SEQ ID NO: 3.

3. The isolated nucleic acid molecule of claim 1, wherein said MUC17 polypeptide has the amino acid sequence of SEQ ID NO: 4.

4. The isolated nucleic acid molecule of claim 1, wherein said nucleotide sequence is SEQ ID NO: 1.

5. The isolated nucleic acid molecule of claim 1, wherein said nucleotide sequence is sequence of SEQ ID NO: 2.

6. The isolated nucleic acid of claim 1, which is DNA.

7. The isolated nucleic acid of claim 6, which is a cDNA encoding a MUC17 polypeptide.

8. The isolated nucleic acid of claim 6, which is a gene comprising introns and exons, said exons encoding said MUC17 polypeptide of SEQ ID NO: 3 or SEQ ID NO: 4, and said nucleic acid sequence having the intron exon junctions of Table I.

9. An isolated RNA molecule transcribed from the nucleic acid of claim 6.

10. An isolated plasmid comprising the nucleic acid molecule of claim 1.

11. An isolated vector comprising the nucleic acid molecule of claim 1.

12. An isolated retroviral vector comprising the nucleic acid molecule of claim 1.

13. An isolated host cell comprising the nucleic acid molecule of claim 1.

14. The isolated host cell of claim 13, wherein said host cell is selected from the group consisting of bacterial, fungal, mammalian, insect and plant cells.

15. The isolated host cell of claim 13, wherein said nucleic acid molecule is provided in a plasmid and is operably linked to mammalian regulatory elements in reverse, antisense orientation.

16. A method for diagnosing pancreatic cancer in a patient comprising:
a) measuring the level of the nucleic acid molecule encoding MUC17 of claim 1 in a biological sample from said patient; and
b) comparing said level of said MUC 17 nucleic acid molecule from said patient with that from a healthy subject, wherein an elevation of said level of said MUC17 nucleic acid molecule from said patient is indicative that said patient has pancreatic cancer.

17. The method of claim 16, wherein said MUC17 nucleic acid molecule is an mRNA which encodes a MUC17 protein having a sequence of SEQ ID NO: 3.

18. The method of claim 16, wherein said MUC17 nucleic acid molecule is an mRNA which encodes a MUC17 protein having a sequence of SEQ ID NO: 4.

19. The method of claim 16, further comprising:
c) measuring expression levels MUC4 and/or MUC12 in said biological sample from said patient; and
d) comparing said expression levels MUC4 and/or MUC12 from said patient with that from said healthy subject, wherein an elevation of said expression levels of MUC4 and/or MUC12 is indicative that said patient has pancreatic cancer.

20. A kit for diagnosing pancreatic cancer in a patient comprising:
a) means for isolating RNAs from a biological sample;
b) means for detecting and quantifying the nucleic acid molecule of claim 1, comprising at least one nucleic acid probe consisting of a sequence selected from the group consistina of SEQ ID NO: 13, SEQ ID NO: 14, and SEQ ID NO: 15; and optionally
c) instructional material.

21. The kit of claim 20, wherein said nucleic acid probe further comprises a detectable label.

22. The kit of claim 20, wherein said mRNA encodes a MUC17 protein with a sequence of SEQ ID NO: 3.

23. The kit of claim 20, wherein said mRNA encodes a MUC17 protein with a sequence of SEQ ID NO: 4.