EP1255766A2 - Acides nucleiques, proteines et anticorps - Google Patents

Acides nucleiques, proteines et anticorps

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Publication number
EP1255766A2
EP1255766A2 EP01910329A EP01910329A EP1255766A2 EP 1255766 A2 EP1255766 A2 EP 1255766A2 EP 01910329 A EP01910329 A EP 01910329A EP 01910329 A EP01910329 A EP 01910329A EP 1255766 A2 EP1255766 A2 EP 1255766A2
Authority
EP
European Patent Office
Prior art keywords
seq
polypeptide
sequence
polynucleotides
polynucleotide
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP01910329A
Other languages
German (de)
English (en)
Inventor
Craig A. Rosen
Steven C. Barash
Steven M. Ruben
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Human Genome Sciences Inc
Original Assignee
Human Genome Sciences Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Human Genome Sciences Inc filed Critical Human Genome Sciences Inc
Priority claimed from PCT/US2001/001324 external-priority patent/WO2001055314A2/fr
Publication of EP1255766A2 publication Critical patent/EP1255766A2/fr
Withdrawn legal-status Critical Current

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Classifications

    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • Sequence Listing is provided as an electronic file (PC002PCT_seqList.txt, 9,710,493 bytes in size, created on January 12, 2001) on four identical compact discs (CD-R), labeled "COPY 1," "COPY 2,” “COPY 3,” and "CRF.”
  • the Sequence Listing complies with Annex C of the Ndministrative Instructions, and may be viewed, for example, on an IBM-PC machine running the MS-Windows operating system by using the V viewer software, version 2000 (see World Wide Web URL: http ://www.fileviewer.com) .
  • the present invention relates to novel digestive system related polynucleotides, the polypeptides encoded by these polynucleotides herein collectively referred to as "digestive system antigens," and antibodies that immunospecifically bind these polypeptides, and the use of such digestive system polynucleotides, antigens, and antibodies for detecting, treating, preventing and/or prognosing disorders of the digestive system, including, but not limited to, the presence of cancer and cancer metastases. More specifically, isolated digestive system nucleic acid molecules are provided encoding novel digestive system polypeptides. Novel digestive system polypeptides and antibodies that bind to these polypeptides are provided.
  • vectors, host cells, and recombinant and synthetic methods for producing human digestive system polynucleotides, polypeptides, and/or antibodies are also provided.
  • the invention further relates to diagnostic and therapeutic methods useful for diagnosing, treating, preventing and/or prognosing disorders related to the digestive system, including cancer, and therapeutic methods for treating such disorders.
  • the invention further relates to screening methods for identifying agonists and antagonists of polynucleotides and polypeptides of the invention.
  • the invention further relates to methods and/or compositions for inhibiting or promoting the production and/or function of the polypeptides of the invention.
  • the Human Digestive System is a collection of specialized organs and body tissues that prepare food for use by hundreds of millions of body cells. Food when eaten cannot reach cells because it cannot pass through ' the intestinal walls to the bloodstream and, if it could would not be in a useful chemical state.
  • the gut modifies food physically and chemically and disposes of unusable waste. Physical and chemical modification (digestion) depends on exocrine and endocrine secretions and controlled movement of food through the digestive tract.
  • the three fundamental processes of the Digestive System are: Secretion (e.g., delivery of enzymes, mucus, ions and the like into the lumen, and hormones into blood), Absorption (e.g., transport of water, ions and nutrients from the lumen, across the epithelium and into blood), and Motility (e.g., contraction's of smooth muscle in the wall of the tube that crush, mix and propel its contents).
  • Secretion e.g., delivery of enzymes, mucus, ions and the like into the lumen, and hormones into blood
  • Absorption e.g., transport of water, ions and nutrients from the lumen, across the epithelium and into blood
  • Motility e.g., contraction's of smooth muscle in the wall of the tube that crush, mix and propel its contents.
  • Control of digestive function is achieved through a combination of electrical and hormonal messages which originate either within the digestive system's own nervous and endocrine systems, as well as from the central nervous sytem and
  • the digestive system is composed of the digestive or alimentary tube and accessory digestive organs, which include the Mouth (e.g., tongue, taste buds, soft palate pharynx, salivary glands, teeth), Esophagus, Stomach, Liver, Gallbladder,
  • Mouth e.g., tongue, taste buds, soft palate pharynx, salivary glands, teeth
  • Esophagus Stomach, Liver, Gallbladder
  • Pancreas, Small Intestine e.g., duodenum, jejunum, and ileum
  • Large Intestine e.g., duodenum, jejunum, and ileum
  • Dysphagia may be prominent in cases of degenerative disease of the central nervous system, especially of the ganglia at the base of the brain.
  • Congenital disorders of the esophagus are most often seen in infancy, primarily as a failure to develop normal passageways.
  • the lower end of the esophagus is subject to various developmental anomalies that shorten the organ so that the stomach is pulled up into the thoracic cavity. Anomalies of the diaphragm may contribute to a similiar outcome.
  • Inflammatory disorders of the esophagus result from a variety of causes; for example, ingestion of noxious materials (e.g., corrosive esophagitis), lodgment of foreign bodies, or a complex of events associated with reflux of gastric contents from the stomach into the lower esophagus (e.g., peptic esophagitis).
  • noxious materials e.g., corrosive esophagitis
  • lodgment of foreign bodies e.g., a complex of events associated with reflux of gastric contents from the stomach into the lower esophagus (e.g., peptic esophagitis).
  • Benign tumors of the esophagus originate in the submucosal tissues and principally are leiomyomas (tumors composed of smooth muscle tissue) or lipomas (tumors composed of adipose, or fat, tissues).
  • Malignant tumors are either epidermal cancers, made up of unorganized aggregates of cells, or adenocarcinomas, in which there are gland-like formations.
  • Cancers arising from squamous tissues are found at all levels of the organ, whereas adenocarcinomas are more common at the lower end where a number of glands of gastric origin are normally present.
  • the prognosis is poor because diagnosis is difficult and the tumor has usually been growing for one or two years before symptoms are apparent.
  • Any disorder that affects the power of coordination of the stomach muscles is capable of producing symptoms ranging from those that are mildly unpleasant (e.g., anorexia and nausea) to others that are life-threatening.
  • the intrinsic muscles of the stomach are innervated by branches of the vagus nerves, which travel along the esophagus from their point of emergence in the brain stem. Severing these nerves or altering their function by the use of anticholinergic medication may produce temporary or more prolonged change in the ability of the stomach to empty itself. Gastric retention may result from the degeneration of the nerves to the stomach that can result from diabetes mellitus.
  • ulcerative diseases which involve mucosal breakdown either confined ' to the superficial layers of the mucosa (e.g., an erosion) or extending through the intrinsic layer of muscle of the mucosa into the tissues below (e.g., an ulcer).
  • the circumstances that contribute to mucosal injury and ulcer formation include physical and chemical trauma that result from hot fluids and food, aspirin and other drugs, irritating spices, and pickling fluids.
  • genetic factors are involved in the development of ulcers.
  • the complications of peptic ulcers are hemorrhage, perforation, and obstruction of the outlet of the stomach (pyloric stenosis) by scarfing of the duodenal bulb or of the pyloric channel.
  • gastritis A diffuse inflammation of the stomach lining, gastritis, is usually an acute process caused by contaminated food, alcohol abuse, or by bacterial- or viral-induced inflammation of the gastrointestinal tract (gastroenteritis).
  • the other form of gastritis is gastric atrophy, in which the thickness of the mucosa is diminished. Diffuse gastric atrophy leads to partial loss of the glands and secreting cells throughout the stomach and may be • associated with iron-deficiency anemia.
  • Malignant tumors of the stomach are common and are probably a result of both genetic and environmental factors. Gastric cancer affects men more often than women and accounts for about 20 percent of all deaths from cancers of the gastrointestinal tract in the United States. Other malignant tumors that involve the stomach are tumors ordinarily made up of lymphoid and connective tissue. Benign tumors, especially leiomyomas, are common and may, when large, cause massive hemorrhage. Polyps of the stomach are not common except in the presence of gastric atrophy.
  • the extremely common disorder known as the irritable bowel syndrome is probably due to a disturbance of the motility of the whole intestinal tract.
  • the symptoms vary from watery diarrhea to constipation and the passage of stools with difficulty.
  • an excess of mucus is often observed in the stools.
  • the irritable bowel syndrome may be due to an allergy to a particular foodstuff.
  • the syndrome may develop following an infection such as bacillary dysentery, after which the small intestine remains irritable for many months.
  • a further disorder, malabsorption occurs when the small intestine is unable to transport properly broken down products of digestive materials from the lumen of the intestine into the lymphatics or mesenteric veins, where they are distributed to the rest of the body. Defects in transport occur either because the absorptive cells of the intestine lack certain enzymes, whether by birth defect or by acquired disease, or because they are hindered in their work by other disease processes that infiltrate the tissues, disturb motility, permit bacteria to overpopulate the bowel, or block the pathways over which transport normally proceeds.
  • a malabsorption disorder of unknown cause, tropical sprue is associated with partial atrophy of the mucosa of the small intestine.
  • Meckel's diverticulum is a common congenital malformation that occurs when the duct leading from the navel to the small intestine in the fetus fails to atrophy and close.
  • Another congenital problem in the small intestine is the presence of multiple diverticula, or outpouchings of mucosa and serosa.
  • a third congenital malformation is a failure of complete rotation of the small and large intestine, which is a normal step in the development of the fetus. This can result in abnormal intestinal attachments with a subsequent risk of obstruction when the intestine twists around the attachments.
  • disorders of the small intestine also include bacterial and parasitic infections.
  • Traveler's diarrhea e.g., diarrhea which is watery, accompanied by cramps, and lasts a few days
  • diarrhea generally disappears spontaneously with abstention from food accompanied by drinking of nonalcoholic fluids.
  • Species of Salmonella that cause typhoid and paratyphoid remain endemic in some contries and, together with Shigella, are occasional causes of epidemics in institutions.
  • Cholera caused by Vibrio cholerae, is endemic to Southeast Asia and periodically becomes pandemic.
  • parasitism In equatorial countries, parasitism is endemic, with Roundworms, tapeworms, amoebae, hookworms, strongyloides, threadworms, and blood flukes (schistosomiasis) being the main types of parasites.
  • Roundworms, or Ascariasis lumbricoides interfere with the absorption of fat and protein in the intestine, which causes diarrhea.
  • Hookworm, or Ancylostoma duodenale infection deplete the body of nutrients, and a major effect is severe chronic iron-deficiency anemia.
  • Threadworms, or Enterobius vermicularis live mainly in the cecum and cause anal itching.
  • Common tapeworms are Taenia saginata, found in beef, and T.
  • Appendicitis is an inflammation of the vermiform appendix that may be caused by infection or partial or total obstruction. Chronic inflammations of the small intestine include tuberculosis and regional enteritis (Crohn's disease).
  • Celiac disease causes damage to the mucosa of the small intestine, though it is not clear whether it is caused by an immune reaction, or an inability to break down a toxic protein, gluten, to smaller peptide fractions.
  • Studies of the immune function of those with celiac disease suggest that at least a major part of the process is a delayed hypersensitivity reaction and that the morphological changes are correlated with the presence of circulating antibodies to gluten.
  • the mucosal reaction results in progressive atrophy, with dwarfing, if not complete disappearance, of the micro villi and villi that line the intestinal tract.
  • a disease that is analogous to achalasia of the esophagus is an idiopathic condition called aganglionic megacolon, or Hirschsprung's disease.
  • Shigella species may attack the mucous membrane of the colon and produce an intense but rather superficial hemorrhage; Salmonella species may damage the lymph follicles of the colon, but do not produce a generalized inflammation of the colon; cytomegalic virus can cause a severe colitis producing ulcerations; Lymphopathia venereum can cause a more generalized and superficial colitis; and Entamoeba histolytica lodge in the cecum and ascending colon, undermine the mucosal coat, and may create large ulcerations that bleed impressively.
  • ulcerative colitis The most common form of chronic colitis, ulcerative colitis, is idiopathic. It varies from a mild inflammation of the mucosa of the rectum, giving rise to excessive mucus and some spotting of blood in the stools, to a severe, sudden, intense illness, with destruction of a large part of the colonic mucosa, considerable blood loss, toxemia and, less commonly, perforation.
  • the most common variety affects only the rectum and sigmoid colon and is characterized by diarrhea and the passage of mucus. Apart from the greater tendency for fistulas to form and for the wall of the intestine to thicken until the channel is obstructed, Crohn's disease is distinguishable from ulcerative colitis by microscopic findings.
  • Crohn's disease the maximum damage occurs beneath the mucosa, and lymphoid conglomerations, known as granulomata, are formed in the submucosa. Crohn's disease attacks the perianal tissues more often than does ulcerative colitis. Although these two diseases are not common, they are disabling.
  • Tumors of the colon are usually polyps or cancers.
  • a peculiar form of polyp is the villous adenoma, often a slowly growing, fernlike structure that spreads along the surface of the colon for some distance.
  • cancer of the colon is a more common tumor than is cancer of the stomach, and it occurs about equally in both sexes. Cancers compress the colonic lumen to produce obstruction, they attach to neighbouring structures to produce pain, and they perforate to give rise to peritonitis. Cancers also may metastasize to distant organs before local symptoms appear.
  • Anorectal disorders related to defecation are more common in the Western world than elsewhere. These disorders usually take the form of fissures (cuts or cracks in the skin or mucous membrane) at the junction of the anal mucous membrane with the skin between the thighs. Anal fistulas sometimes occur as complications of serious bowel disease, as in tuberculosis or Crohn's disease of the bowel, or in certain parasitic diseases.
  • a more general disorder is the enlargement of veins of the rectum and anus to form external or internal hemorrhoids. Hemorrhoids protrude, are associated with anal itching and pain, and bleed, especially when they come in contact with hard stools.
  • liver diseases can affect one of the three functional components of the liver: the hepatocyte (liver cell) itself, the bile secretory (cholangiolar) apparatus, or the blood vascular system.
  • Most acute liver diseases are self-limited, and liver functioning returns to normal once the causes are removed or eliminated. In some cases, however, the acute disease process destroys massive areas of liver tissue in a short time, leading to extensive death (necrosis) of hepatic cells and often to death of the patient. Hepatitis may result from viral infections or toxic damage from drugs or poisons.
  • hepatocellular damage is severe enough to destroy entire acini (clusters of lobules), they are often replaced with fibrous scar tissue. Bile canaliculi and hepatocytes regenerate in an irregular fashion adjacent to the scar tissue and result in a chronic condition called cirrhosis of the liver. Where inflammatory activity continues after the onset of cirrhosis, the disorderly regeneration of hepatocytes and cholangioles may lead to the development of hepatocellular or cholangiolar cancer.
  • hepatitis virus A HAV
  • HBV hepatitis virus B
  • NANB hepatitis virus non-A, non-B
  • Hepatitis B virus is present throughout the world in asymptomatic human carriers who may or may not have ongoing liver disease and formerly, the disease was widely spread by the transfusion of whole blood or blood products.
  • the hepatitis NANB virus has not been isolated, and currently is the major cause of posttransfusion hepatitis.
  • the symptoms characteristic of the acute hepatitis caused by the HAV, HBV, and NANB viruses are essentially indistinguishable from one another.
  • Acute hepatitis also may be caused by the overconsumption of alcohol or other poisons, such as commercial solvents (e.g., carbon tetrachloride), acetaminophen, and certain fungi.
  • alcohol or other poisons such as commercial solvents (e.g., carbon tetrachloride), acetaminophen, and certain fungi.
  • Such agents are believed to cause hepatitis when the formation of their toxic intermediate metabolites in the liver cell (phase I reactions) is beyond the capacity of the hepatocyte to conjugate, or join them with another substance for detoxification (phase II reactions) and excretion. As long as the levels of these agents are small enough to permit complete phase I and phase II reactions, there is no damage to the liver cell.
  • Acute canalicular (cholestatic) hepatitis is most commonly caused by certain drugs, such as chlorpromazine, that lead to idiosyncratic reactions or, at times, by hepatitis viruses.
  • Acute congestive liver disease usually results from the sudden . engorgement of the liver by fluids after congestive heart failure.
  • Chronic active hepatitis the result of unresolved acute injury, is associated with ongoing liver damage.
  • a milder form of chronic disease called persistent hepatitis, does not appear to lead to progressive liver damage despite evidence of a continuing mild inflammation.
  • These conditions may result from viral hepatitis, drug- induced hepatitis, autoimmune liver diseases (lupoid hepatitis), or congenital abnormalities.
  • a prominent autoimmune liver disease is Wilson's disease, which is caused by abnormal deposits of large amounts of copper in the liver.
  • Granulomatous hepatitis a condition in which localized areas of inflammation (granulomas) appear in any portion of the liver lobule, is a type of inflammatory disorder associated with many systemic diseases, including tuberculosis, sarcoidosis, schistosomiasis, and certain drug reactions. Granulomatous hepatitis rarely leads to serious interference with hepatic function, although it is often chronic.
  • liver injury The end result of many forms of chronic liver injury is cirrhosis, or scarring of liver tissue in reponse to previous acinar necrosis and irregular regeneration of liver nodules and bile ducts.
  • congenital disorders producing cirrhosis are Wilson's disease, hemochromatosis (over-deposition of iron pigment), cystic fibrosis, biliary atresia (congenital absence of a part of the bile ducts), and alpha 1-antitrypsin deficiency, or the congenital absence of a proteolytic enzyme inhibitor that results in the accumulation of abnormal forms of carbohydrate in hepatocytes.
  • cirrhosis of the liver most commonly results from chronic heavy intake of alcohol, while chronic viral hepatitis is probably the leading cause of cirrhosis in underdeveloped countries.
  • Primary biliary cirrhosis a widespread, though uncommon, autoimmune inflammatory disease of bile ducts, is a disorder primarily affecting middle-aged and older women.
  • Secondary biliary cirrhosis results from chronic obstruction or recurrent infection in the extrahepatic bile ducts caused by strictures, . gallstones, or tumors. Infestation of the biliary tract with a liver fluke, Clonorchis sinensis, is a cause of secondary biliary cirrhosis in Asia.
  • Hepatic encephalopathy refers to the changes in the brain that occur in patients with advanced acute or chronic liver disease. If liver cells are damaged, certain substances that are normally cleansed from the blood by the healthy liver are not removed. In the case of cirrhosis, blood from the portal system is not exposed to functioning hepatocytes because it is transported through blood vessels in the liver that do not run through regenerating nodules of hepatocytes, owing to the atypical growth inherent in the cirrhotic process. These products of cell metabolism are primarily .
  • Portal hypertension the increased pressure in the portal vein and its tributaries that is the result of impediments to venous flow into the liver, is brought about by the scarring characteristic of the cirrhotic process.
  • the increased pressure causes feeders of the portal vein to distend markedly, producing varices, or dilations of the veins.
  • varices When varices are located in superficial tissues, they may rupture and bleed profusely. Two such locations are the lower esophagus and the perianal region.
  • the accumulation of fluid in the abdominal cavity, or ascites, is related to portal hypertension, significant reduction in serum albumin, and renal retention of sodium.
  • liver abscesses result from the spread of infection from the biliary tract or from other parts of the body, especially the appendix and the pelvic organs. Specific liver abscesses also result from infections with the intestinal parasite Entamoeba histolytica.
  • stcholecystectomy syndrome comprises painful attacks, often resembling preoperative symptoms, that occasionally occur following the surgical removal of gallstones and the gallbladder. These attacks may be related to intermittent muscular spasms of the sphincter of Oddi or of the bile ducts.
  • Cancer of the biliary tract is rare but may occur in almost any area, including the gallbladder, the hepatic ducts, the common bile duct, or the ampulla of Vater.
  • congenital cysts and parasitic infections such as liver flukes, seem to lead to increased risks.
  • Persons with extensive chronic ulcerative colitis also show a greater than normal incidence of bile duct carcinoma.
  • Jaundice or yellowing of the skin, scleras, and mucous membranes, occurs whenever the level of bilirubin in the blood is significantly above normal. This condition is evident in three different types of disorders including, unconjugated, or hemolytic, jaundice; hepatocellular jaundice; and cholestatic, or obstructive jaundice. Unconjugated jaundice results when the amount of bilirubin produced from hemoglobin by the destruction of red blood cells or muscle tissue (myoglobin) overwhelms the normal capacity of the liver to transport it or when the ability of the liver to conjugate normal amounts of bilirubin into bilirubin diglucuronide is significantly reduced by inadequate intracellular transport or enzyme systems.
  • Hepatocellular jaundice arises when liver cells are damaged so severely that their ability to transport bilirubin diglucuronide into the biliary system is reduced, allowing some of this yellow pigment to regurgitate into the bloodstream.
  • Cholestatic jaundice occurs when essentially normal liver cells are unable to transport bilirubin either through the hepatocytic-bile capillary membrane, because of damage in that area, or through the biliary tract, because of anatomical obstructions (e.g., atresias, gallstones, cancer).
  • pancreatitis Inflammation of the pancreas, or pancreatitis, is probably the most common disease of this organ. The disorder may be confined to either singular or repeated acute episodes, or it may become a chronic disease. There are many factors associated with the onset of pancreatitis, including direct injury, certain drugs, viral infections, heredity, hyperlipidemia (increased levels of blood fats), and congenital derangements of the ductal system. Localized, severe abdominal and midback pain resulting from enzyme leakage, tissue damage, and nerve irritation is the most common symptom of acute pancreatitis. In severe cases, respiratory failure, shock, and even death may occur. Chronic pancreatitis rarely follows repeated acute attacks.
  • the present invention relates to novel digestive system related polynucleotides, the polypeptides encoded by these polynucleotides herein collectively referred to as
  • digestive system antigens and antibodies that immunospecifically bind these polypeptides, and the use of such digestive system polynucleotides, antigens, and antibodies for detecting, treating, preventing and/or prognosing disorders of the digestive system, including, but not limited to, the presence of cancer and cancer metastases. More specifically, isolated digestive system nucleic acid molecules are provided encoding novel digestive system polypeptides. Novel digestive system polypeptides and antibodies that bind to these polypeptides are provided. Also provided are vectors, host cells, and recombinant and synthetic methods for producing human digestive system polynucleotides, polypeptides, and/or antibodies.
  • the invention further relates to diagnostic and therapeutic methods useful for diagnosing, treating, preventing and/or prognosing disorders related to the digestive system, including cancer, and therapeutic methods for treating such disorders.
  • the invention further relates to screening methods for identifying agonists and antagonists of polynucleotides and polypeptides of the invention.
  • the invention further relates to methods and/or compositions for inhibiting or promoting the production and/or function of the polypeptides of the invention.
  • Table 1A summarizes some of the polynucleotides encompassed by the invention (including cDNA clones related to the sequences (Clone ID NO:Z), contig sequences (contig identifier (Contig ID:) and contig nucleotide sequence identifier (SEQ ID NO:X)) and further summarizes certain characteristics of these polynucleotides and the polypeptides encoded thereby.
  • the first column provides a unique clone identifier, "Clone ID NO:Z”, for a cDNA plasmid related to each digestive system associated contig sequence disclosed in Table 1A.
  • the second column provides a unique contig identifier, "Contig ID:" for each of the contig sequences disclosed in Table 1A.
  • the third column provides the sequence identifier, "SEQ ID NO:X' ⁇ for each of the contig polynucleotide sequences disclosed in Table 1A.
  • the fourth column "ORF (From-To)" provides the location (i.e., nucleotide position numbers) within the polynucleotide sequence of SEQ ID NO:X that delineate the preferred open reading frame (ORF) shown in the sequence listing and referenced in Table 1 as SEQ ID NO:Y (column 5).
  • Column 6 lists residues comprising predicted epitopes contained in the polypeptides encoded by each of the preferred ORFs (SEQ ID NO: ⁇ ).
  • stomach associated polypeptides of the invention comprise, or alternatively consist of, one, two, three, four, five or more of the predicted epitopes described in Table 1A. It will be appreciated that depending on the analytical criteria used to predict antigenic determinants, the exact address of the determinant may vary slightly.
  • Column 7, “Tissue Distribution” shows the expression profile of tissue, cells, and/or cell line libraries which express the polynucleotides of the invention. The first number in column 7 (preceding the colon), represents the tissue/cell source identifier code corresponding to the code and description provided in Table 4.
  • tissue/cell source identifier codes in which the first two letters are not "AR” represent the number of times a sequence corresponding to the reference polynucleotide sequence (e.g., SEQ ID NO:X) was identified in the tissue/cell source.
  • tissue/cell source identifier codes in ' which the first two letters are "AR” designate information generated- using DNA array technology. Utilizing this technology, cDNAs were amplified by PCR and then transferred, in duplicate, onto the array. Gene expression was assayed through hybridization of first strand cDNA probes to the DNA array.
  • cDNA probes were generated from total RNA extracted from a variety of different tissues and cell lines. Probe synthesis was performed in the presence of 33 P dCTP, using oligo(dT) to prime reverse transcription. After hybridization, high stringency washing conditions were employed to remove non-specific hybrids from the array. The remaining signal, emanating from each gene target, was measured using a Phosphorimager. Gene expression was reported as Phosphor Stimulating Luminescence (PSL) which reflects the level of phosphor signal generated from the probe hybridized to each of the gene targets represented on the array. A local background signal subtraction was performed before the total signal generated from each array was used to normalize gene expression between the different hybridizations.
  • PSL Phosphor Stimulating Luminescence
  • Table 1A summarizes additional polynucleotides encompassed by the invention (including cDNA clones related to the sequences (Clone ID NO :Z), contig sequences (contig identifier (Contig ID:) contig nucleotide sequence identifiers (SEQ ID NO:X)), and genomic sequences (SEQ ID NO:B).
  • the first column provides a unique clone identifier, "Clone ID NO:Z”, for a ⁇ cDNA clone related to each contig sequence.
  • the second column provides the sequence identifier, "SEQ ID NO:X”, for each contig sequence.
  • the third column provides a unique contig identifier, "Contig ID:” for each contig sequence.
  • the fourth column provides a BAC identifier "BAC ID NO:A” for the BAC clone referenced in the corresponding row of the table.
  • the fifth column provides the nucleotide sequence identifier, "SEQ ID NO:B” for a fragment of the BAC clone identified in column four of the corresponding row . of the table.
  • the sixth column provides the location (i.e., nucleotide position numbers) within the polynucleotide sequence of SEQ ID NO:B which delineate certain polynucleotides of the invention that are also exemplary members of polynucleotide sequences that encode polypeptides of the invention (e.g., polypeptides containing amino acid sequences encoded by the polynucleotide sequences delineated in column six, and fragments and variants thereof).
  • Table 2 summarizes homology and features of some of the polypeptides of the invention.
  • the first column provides a unique clone identifier, "Clone ID NO:Z”, corresponding to a cDNN disclosed in Table IN.
  • the second column provides the unique contig identifier, "Contig ID:” corresponding to contigs in Table IN and allowing for correlation with the information in Table IN.
  • the third column provides the sequence identifier, "SEQ ID ⁇ O:X", for the contig polynucleotide sequences.
  • the fourth column provides the analysis method by which the homology/identity disclosed in the row was determined. Comparisons were made between polypeptides encoded by the polynucleotides of the invention and either a non-redundant protein database (herein referred to as "NR"), or a database of protein families (herein referred to as "PFAM”) as further described below.
  • the fifth column provides a description of PFAM/NR hits having significant matches to a polypeptide of the invention.
  • polypeptides of the invention comprise, or alternatively consist of, an amino acid sequence encoded by the polynucleotides in SEQ ID NO:X as delineated in columns 8 and 9, or fragments or variants thereof.
  • Table 3 provides polynucleotide sequences that may be disclaimed according to certain embodiments of the invention.
  • the first column provides a unique clone identifier, "Clone ID NO:Z”, for a cDNA clone related to digestive system associated contig sequences disclosed in Table 1A.
  • the second column provides the sequence identifier, "SEQ ID.NO:X”, for contig polynucleotide sequences disclosed in Table 1A.
  • the third column provides the unique contig identifier, "Contig ID”, for contigs disclosed in Table 1A.
  • the fourth column provides a unique integer 'a' where 'a' is any integer between 1 and .the final nucleotide minus 15 of SEQ ID NO:X, represented as "Range of a", .and the fifth column provides a unique integer 'b' where 'b' is any integer between 15 and the final nucleotide of SEQ ID NO:X, represented as "Range of b", where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:X, and where b is greater than or equal to a + 14.
  • polynucleotides shown as SEQ ID NO:X the uniquely defined integers can be substituted into the general formula of a-b, and used to describe polynucleotides which may be preferably excluded from the invention.
  • preferably excluded from the polynucleotides of the invention are at least one, two, three, four, five, ten, or more of the polynucleotide sequence(s) having the accession number(s) disclosed in the sixth column of this Table (including for example, published sequence in connection with a particular BAC clone).
  • preferably excluded from the invention are the specific polynucleotide sequence(s) contained in the clones corresponding to at least one, two, three, four, five, ten, or more of the available material having the accession numbers identified in the sixth column of this Table (including for example, the actual sequence contained in an identified BAC clone).
  • Table 4 provides a key to the tissue/cell source identifier code disclosed in Table 1A, column 7.
  • Column 1 provides the key to the tissue/cell source identifier code disclosed in Table 1A, Column 7.
  • Columns 2-5 provide a description of the tissue or cell source. Codes corresponding to diseased tissues are indicated in column 6 with the word "disease". The use of the word "disease" in column 6 is non-limiting.
  • the tissue or cell source may be specific (e.g. a neoplasm), or may be disease-associated (e.g., a tissue sample from a normal portion of a diseased organ).
  • tissues and/or cells lacking the "disease" designation may still be derived from sources directly or indirectly involved in a disease state or disorder, and therefore may have a further utility in that disease state or disorder.
  • the tissue/cell source is a library
  • column 7 identifies the vector used to generate the library.
  • Table 5 provides a key to the OMIMTM reference identification numbers disclosed in Table 1A, column 9.
  • OMIM reference identification numbers (Column 1) were derived from Online Mendelian Inheritance in Man (Online Mendelian Inheritance in Man, OMIMTM. McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine, (Bethesda, MD) 2000. World Wide Web URL: http://www.ncbi.nlm.nih.gov/omim/).
  • Column 2 provides diseases associated with the cytologic band disclosed in Table 1 A, column 8, as determined from the Morbid Map database. [047] Table.
  • Table 6 summarizes ATCC Deposits, Deposit dates, and ATCC designation numbers of deposits made with the ATCC in connection with the present application.
  • Table 7 shows the cDNA libraries sequenced, tissue source description, vector information and ATCC designation numbers relating to these cDNA libraries.
  • Table 8 provides a physical characterization of clones encompassed by the invention. The first column provides the unique clone identifier, "Clone ID NO:Z", for certain cDNA clones of the invention, as described in Table 1 A. The second column provides the size of the cDNA insert contained in the corresponding cDNA clone.
  • isolated refers to material removed from its original environment (e.g., the natural environment if it is naturally occurring), and thus is altered “by the hand of man” from its natural state.
  • an isolated polynucleotide could be part of a vector or a composition of matter, or could be contained within a cell, and still be “isolated” because that vector, composition of matter, or particular cell is not the original environment of the polynucleotide.
  • isolated does not refer to genomic or cDNA libraries, whole cell total or mRNA preparations, genomic DNA preparations (including those separated by electrophoresis and transferred onto blots), sheared whole cell genomic DNA preparations or other compositions where the art demonstrates no distinguishing features of the polynucleotide sequences of the present invention.
  • a "polynucleotide” refers to a molecule having a nucleic acid sequence encoding SEQ ID NO:Y or a fragment or variant thereof, a nucleic acid sequence contained in SEQ ID NO:X (as described in column 3 of Table 1A) or the complement thereof, a cDNA sequence contained in Clone ID NO:Z (as described in column 1 of Table 1A and contained within a library deposited with the ATCC); a nucleotide sequence encoding the polypeptide encoded by a nucleotide sequence in SEQ ID NO:B as defined in column 6.
  • the polynucleotide can contain the nucleotide sequence of the full length cDNA sequence, including the 5' and 3' untranslated sequences, the coding region, as well as fragments, epitopes, domains, and variants of the nucleic acid sequence.
  • polypeptide refers to a molecule having an amino acid sequence encoded by a polynucleotide of the invention as broadly defined (obviously excluding poly-Phenylalanine or poly-Lysine peptide sequences which result from translation of a polyA tail of a sequence corresponding to a cDNA).
  • a "digestive system antigen” refers collectively to any polynucleotide disclosed herein (e.g., a nucleic acid sequence contained in SEQ ID NO:X of the complement therof, or cDNA sequence contained in Clone ID NO:Z, or a nucleotide sequence encoding the polypeptide encoded by a nucleotide sequence in SEQ ID NO:B as defined in column 6 of Table IB, or a nucleotide coding sequence in • SEQ ID NO:B as defined in column 6 of Table IB or the complement thereof and fragments or variants thereof as described herein) or any polypeptide disclosed herein (e.g., an amino acid sequence contained in SEQ ID NO:Y, an amino acid sequence encoded by SEQ ID NO:X, or the complement thereof, an amino acid sequence encoded by the cDNA sequence contained in Clone ID NO:Z, an amino acid sequence encoded by SEQ ID NO:B, or the complement thereof, and fragments or
  • SEQ ID NO:X was often generated by overlapping sequences contained in multiple clones (contig analysis).
  • a representative clone containing all or most of the sequence for SEQ ID NO:X is deposited at Human Genome Sciences, Inc. (HGS) in a catalogued and archived library.
  • HGS Human Genome Sciences, Inc.
  • each clone is identified by a cDNA Clone ID (identifier generally referred to herein as Clone ID NO:Z).
  • Clone ID NO:Z identifier generally referred to herein as Clone ID NO:Z.
  • Each Clone ID is unique to an individual clone and the Clone ID is all the information needed to retrieve a given clone from the HGS library.
  • ATCC American Type Culture Collection
  • Library names contain four characters, for example, "HTWE.”
  • the name of a cDNA clone (Clone ID NO:Z) isolated from that library begins with the same four characters, for example "HTWEP07".
  • Table 1A correlates the Clone ID NO:Z names with SEQ ID NO:X.
  • SEQ ID NO:X the Clone ID NO:Z names with SEQ ID NO:X.
  • Tables 1A, 6 and 7 to determine the corresponding Clone ID NO:Z, which library it came from and which ATCC deposit the library is contained in.
  • it is possible to retrieve a given cDNA clone from the source library by techniques known in the art and described elsewhere herein.
  • the ATCC is located at 10801 University Boulevard, Manassas, Virginia 20110-2209, USA.
  • the ATCC deposits were made pursuant to the terms of the Budapest Treaty on the international recognition of the deposit of microorganisms for the purposes of patent procedure.
  • the polynucleotides of the invention are at least 15, at least 30, atleast 50, at least 100, at least 125, at least 500, or at least 1000 continuous nucleotides but are less than or equal to 300 kb, 200 kb, 100 kb, 50 kb, 15 kb, 10 kb, 7.5 kb, 5 kb, 2.5 kb, 2.0 kb, or 1 kb, in length.
  • polynucleotides of the invention comprise a portion of the coding sequences, as disclosed herein, but do not comprise all or a portion of any intron.
  • the polynucleotides comprising coding sequences do not contain coding sequences of a genomic flanking gene (i.e., 5' or 3' to the gene of interest in the genome). In other embodiments, the polynucleotides of the invention 'do not contain the coding sequence of more than 1000, 500, 250, 100, 50, 25, 20, 15, 10, 5, 4, 3, 2, or 1 genomic flanking gene(s).
  • a "polynucleotide” of the present invention also includes those polyn ⁇ cleotides capable of hybridizing, under stringent hybridization conditions, to sequences contained in SEQ ID NO:X, or the complement thereof (e.g., the complement of any one, two, three, four, or more of the polynucleotide fragments described herein), the polynucleotide sequence delineated in columns 8 and 9 of Table 2 or the complement thereof, and/or cDNA sequences contained in Clone ID NO:Z (e.g., the complement of any one, two, three, four, or more of the polynucleotide fragments, or the cDNA clone ' within the pool of cDNA clones deposited with the ATCC, described herein) and/or the polynucleotide sequence delineated in column 6 of Table IB or the complement thereof.
  • “Stringent hybridization conditions” refers to an overnight incubation at 42 degree C in a solution comprising 50% formamide, 5x SSC (750 mM NaCl, 75 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5x Denhardt's solution, 10% dextran sulfate, and 20 ⁇ g/ml denatured, sheared salmon sperm DNA, followed by washing the filters in O.lx SSC at about 65 degree C.
  • nucleic acid molecules that hybridize to the polynucleotides of the present invention at lower stringency hybridization conditions.
  • Changes in the stringency of hybridization and signal detection are primarily accomplished through the manipulation of formamide concentration (lower percentages of formamide result in lowered stringency), salt conditions, or temperature.
  • washes performed following stringent hybridization can be done at higher salt concentrations (e.g. 5X SSC).
  • blocking reagents include Denhardt's reagent, BLOTTO, heparin, denatured salmon sperm DNA, and commercially available proprietary formulations.
  • the inclusion of specific blocking reagents may require, modification of the hybridization conditions described above, due to problems with compatibility.
  • polynucleotide which hybridizes only to polyA+ sequences (such as any 3' terminal polyN tract of a cD ⁇ A shown in the sequence listing), or to a complementary stretch of T (or U) residues, would not be included in the definition of "polynucleotide,” since such a polynucleotide would hybridize to any nucleic acid molecule containing a poly (N) stretch or the complement thereof (e.g., practically any double-stranded cD ⁇ N clone generated using oligo dT as a primer).
  • the polynucleotide of the present invention can be composed of any polyribonucleotide or polydeoxribonucleotide, which may be unmodified R ⁇ N or D ⁇ N or modified R ⁇ N or D ⁇ N.
  • polynucleotides can be composed of single- and double-stranded D ⁇ N, D ⁇ N that is a mixture of single- and double- stranded regions, single- and double-stranded R ⁇ N, and R ⁇ N that is mixture of single- and double-stranded regions, hybrid molecules comprising D ⁇ A and R ⁇ A that may be single-stranded or, more typically,. double-stranded or a mixture of single- and double-stranded regions.
  • polynucleotide can be composed of triple- stranded regions comprising R ⁇ A or D ⁇ A or both R ⁇ A and D ⁇ A.
  • a polynucleotide may also contain one or more modified bases or D ⁇ A or R ⁇ A backbones modified for stability or for other reasons.
  • Modified bases include, for example, tritylated bases and unusual bases such as inosine.
  • D ⁇ A and R ⁇ A thus, "polynucleotide” embraces chemically, enzymatically, or metabolically modified forms.
  • the polypeptide of the present invention can be composed of amino acids joined to each other by peptide bonds or modified peptide bonds, i.e., peptide isosteres, and may contain amino acids other than the 20 gene-encoded amino acids.
  • the polypeptides may be modified by either natural processes, such as posttranslational processing, or by chemical modification techniques which are well known in the art. Such modifications are well described in basic texts and in more detailed monographs, as well as in a voluminous research literature. Modifications can occur anywhere in a polypeptide, including the peptide backbone, the amino acid side-chains and the amino. or carboxyl termini.
  • polypeptides may be branched, for example, as a result of ubiquitination, and they may be cyclic, with or without branching. Cyclic, branched, and branched cyclic polypeptides may result from posttranslation natural processes or may be made by synthetic methods.
  • Modifications include acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, pegylation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination.
  • SEQ ID NO:X refers to a polynucleotide sequence described, for example, in
  • SEQ ID NO:Y refers to a polypeptide sequence described in column 5 of Table 1A.
  • SEQ ID NO:X is identified by an integer specified in column 3 of Table 1 A.
  • the polypeptide sequence SEQ ID NO:Y is a translated open reading frame (ORF) encoded by polynucleotide SEQ ID NO:X.
  • Clone ID NO:Z refers to a cDNA clone described in column 1 of Table 1A.
  • a polypeptide having biological activity refers to a polypeptide exhibiting activity similar to, but not necessarily identical to, an activity of a polypeptide of the present invention, including mature forms, as measured in a particular biological assay, with or without dose dependency. In the case where dose dependency does exist, it need not be identical to that of the polypeptide, but rather substantially similar to the dose-dependence in a given activity as compared to the polypeptide of the present invention (i.e., the candidate polypeptide will exhibit greater activity or not more than about 25-fold less and, preferably, not more than about tenfold less activity, and most preferably, not more than about three-fold less activity relative to the polypeptide of the present invention).
  • Table 1A summarizes some of the digestive system associated polynucleotides encompassed by the invention (including contig sequences (SEQ ID NO:X) and clones (Clone ID NO:Z) and further summarizes certain characteristics of these polynucleotides and the polypeptides encoded thereby.
  • the first column in Table 1 A provides a unique "Clone ID NO:Z" for a cDNA clone related to each contig sequence disclosed in Table 1A.
  • This clone ID references the cDNA clone which contains at least the 5' most sequence of the assembled contig and at least a portion of SEQ ID NO:X was determined by directly sequencing the referenced clone.
  • the reference clone may have more sequence than described in the sequence listing or the clone may have less. In the vast majority of cases, however, the clone is believed to encode a full-length polypeptide. In the case where a clone is not full-length, a full-length cDNA can be obtained by methods known in the art and/or as described elsewhere herein.
  • the second column in Table 1A provides a unique "Contig ID” identification for each contig sequence.
  • the third column provides the "SEQ ID NO:X” identifier for each of the digestive system associated contig polynucleotide sequences disclosed in Table 1A.
  • the fourth column, "ORF (From-To)" provides the location (i.e., nucleotide position numbers) within the polynucleotide sequence "SEQ ID NO:X” that delineate the preferred open reading frame (ORF) shown in the sequence listing and referenced in Table 1A, column 5, as SEQ ID NO:Y. Where the nucleotide position number "To" is lower than the nucleotide position number "From”, the preferred ORF • is the reverse complement of the referenced polynucleotide sequence.
  • the fifth column in Table 1A provides the corresponding SEQ ID NO:Y for the polypeptide sequence encoded by the preferred ORF delineated in column 4.
  • the invention provides an amino acid sequence comprising, or. alternatively consisting of, a polypeptide encoded by the portion of SEQ ID NO:X delineated by "ORF (From-To)". . Also provided are polynucleotides encoding such amino acid sequences and the complementary strand thereto.
  • polypeptides of the invention comprise, or alternatively consist of, at least one, two, three, four, five or more of the predicted epitopes as described in Table 1 A.
  • Column 7 in Table 1A provides an expression profile and library code: count for each of the contig sequences (SEQ ID NO:X) disclosed in Table 1A, which can routinely be combined with the information provided in Table 4 and used to determine the normal or diseased tissues, cells, and/or cell line libraries which predominantly express the polynucleotides of the invention.
  • the first number in column 7 represents the tissue/cell source identifier code corresponding to the code and description provided in Table 4.
  • the second number in column 7 represents the number of times a sequence corresponding to the reference polynucleotide sequence was identified in the tissue/cell source.
  • tissue/cell source identifier codes in which the first two letters are "AR” designate information generated using DNA array technology. Utilizing this technology, cDNAs were amplified by PCR and then transferred, in duplicate, onto the array. Gene expression was assayed through hybridization of first strand cDNA probes to the DNA array. cDNA probes were generated from total RNA extracted from a variety of different tissues and cell lines.
  • Probe synthesis was performed in the presence of P dCTP, using oligo(dT) to prime reverse transcription. After hybridization, high stringency washing conditions were employed to remove non-specific hybrids from the array. The remaining signal, emanating from each gene target, was measured using a Phosphorimager. Gene expression was reported as Phosphor Stimulating Luminescence (PSL) which reflects the level of phosphor signal generated from the probe hybridized to each of the gene targets represented on the array. A local background signal subtraction was performed before the total signal generated from each array was used to normalize gene expression between the different hybridizations. The value presented after "[array code]:" represents the mean of the duplicate values, following background subtraction and probe normalization.
  • PSL Phosphor Stimulating Luminescence
  • Each sequence in the UniGene database is assigned to a "cluster"; all of the ESTs, cDNAs, and STSs in a cluster are believed to be derived from a single gene.
  • Chromosomal mapping data is often available for one or more sequence(s) in a UniGene cluster; this data (if consistent) is then applied to the cluster as a whole.
  • it is possible to infer the chromosomal location of a new polynucleotide sequence by determining its identity with a mapped r
  • the first column provides a unique clone identifier, "Clone ID NO:Z”, for a cDNA clone related to each contig sequence.
  • the second column provides the sequence identifier, "SEQ ID NO:X”, for each contig sequence.
  • the third column provides a unique contig identifier, "Contig ID:” for each contig sequence.
  • the fourth column provides a BAC identifier "BAC ID NO:A” for the BAC clone referenced in the corresponding row of the table.
  • the fifth column provides the nucleotide sequence identifier, "SEQ ID NO:B" for a fragment of the BAC clone identified in column four of the corresponding row of the table.
  • the sixth column provides the location (i.e., nucleotide position numbers) within the polynucleotide sequence of SEQ ID NO:B which delineate certain polynucleotides of the invention that are also exemplary members of polynucleotide sequences that encode polypeptides of the invention (e.g., polypeptides containing amino acid sequences encoded by the polynucleotide . sequences delineated in column six, and fragments and variants thereof).
  • Table 2 further characterizes certain encoded polypeptides of the invention, by providing the results of comparisons to protein and protem family databases.
  • the first column provides a unique clone identifier, "Clone ID NO:”, corresponding to a cDNA clone disclosed in Table 1A.
  • the second column provides the unique contig indentifier, "Contig ID:” which allows correlation with the information in Table 1A.
  • the third column provides the sequence identifier, "SEQ ID NO:X”, for the contig .polynucleotide sequences.
  • the fourth column provides the analysis method by which the homology/identity disclosed in the row was determined.
  • the fifth column provides a description of PFam/NR hits having significant matches identified by each analysis.
  • the NR database which comprises the NBRF PIR database, the NCBI
  • GenPept database was made non- redundant using the computer program nrdb2 (Warren Gish, Washington University in Saint Louis).
  • nrdb2 Warren Gish, Washington University in Saint Louis.
  • Each of the polynucleotides shown in Table 1A, column 3 was used to search against the NR database.
  • the computer program BLASTX was used to compare a 6-frame translation of the Query sequence to the NR database (for information about the BLASTX algorithm please see Altshul et al, J. Mol. Biol. 215:403-410 (1990), and Gish et al., Nat. Genet. 3:266-272 (1993)).
  • a description of the sequence that is most similar to the Query sequence (the highest scoring 'Subject') is shown in column five of Table 2 and the database accession number for that sequence is provided in column six.
  • the highest scoring 'Subject' is reported in Table 2 if (a) the estimated probability that the match occurred by chance alone is less than 1.0e-07, and (b) the match was not to a known repetitive element.
  • BLASTX returns alignments of short polypeptide segments of the Query and Subject sequences which share a high degree of similarity; these segments are known as High-Scoring Segment Pairs or HSPs.
  • Table 2 reports the degree of similarity between the Query and the Subject for each HSP as a percent identity in Column 7.
  • the percent identity is determined by dividing the number of exact matches between the two aligned sequences in the HSP, dividing by the number of Query amino acids in the HSP and multiplying by 100.
  • the polynucleotides of SEQ ID NO:X which encode the polypeptide sequence that generates an HSP are delineated by columns 8 and 9 of Table 2.
  • HMM Hidden Markov Model
  • a HMM derived from PFam version 5.2 was said to be a significant match to a polypeptide of the invention if the score returned by HMMER 1.8 was greater than 0.8 times the HMMER 1.8 score obtained with the most distantly related known member of that protein family.
  • the description, of the PFam family which shares a significant match with, a polypeptide of the invention is listed in column 5 of Table 2, and the database accession number of the PFam hit is provided in column 6.
  • Column 7 provides the score returned by HMMER version 1.8 for the alignment.
  • Columns 8 and 9 delineate the polynucleotides of SEQ ID NO:X which encode the polypeptide sequence which shows a significant match to a PFam protein family.
  • the mvention provides a protem comprising, or alternatively consisting of, a polypeptide encoded by the polynucleotides of SEQ ID NO:X delineated in columns 8 and 9 of Table 2. Also provided are polynucleotides encoding such proteins, and the complementary strand thereto..
  • nucleotide sequence SEQ ID NO:X and the translated SEQ ID NO:Y are sufficiently accurate and otherwise suitable for a variety of uses well known in the art and described further below.
  • the nucleotide sequences of SEQ ID NO:X are useful for designing nucleic acid hybridization probes that will detect nucleic acid sequences contained in SEQ ID NO:X or the cDNA contained in Clone ID NO:Z. These probes will also hybridize to nucleic acid molecules in biological samples, thereby enabling immediate applications in chromosome mapping, linkage analysis, . tissue identification and/or typing, and a variety of forensic and diagnostic methods of the invention.
  • polypeptides identified from SEQ ID NO:Y may be used to generate antibodies which bind specifically to these polypeptides, or fragments thereof, and/or to the polypeptides encoded by the cDNA clones identified in, for example, Table 1A.
  • DNA sequences generated by sequencing reactions can contain ⁇ sequencing errors.
  • the errors exist as misidentified nucleotides, or as insertions or deletions of nucleotides in the generated DNA sequence.
  • the erroneously inserted or deleted nucleotides cause frame shifts in the reading frames of the predicted amino acid sequence.
  • the predicted amino acid sequence diverges from the actual amino acid sequence, even though the generated DNA sequence may be greater than 99.9%o identical to the actual DNA sequence (for example, one base insertion or deletion in an open reading frame of over 1000 bases).
  • the present invention provides not only the generated nucleotide sequence identified as SEQ ID NO:X, and a predicted translated amino acid sequence identified as SEQ ID NO:Y, but also a sample of plasmid DNA containing cDNA Clone ID NO:Z (deposited with the ATCC on October 5, 2000, and receiving ATCC designation numbers PTA 2574 and PTA 2575; deposited with the ATCC on January 5, 2001, having the depositor reference numbers TS-1, TS-2, AC-1, and AC-2; and/or as set forth, for example, in Table 1A, 6 and 7).
  • nucleotide sequence of each deposited clone can readily be determined by sequencing the deposited clone in accordance with known methods. Further, techniques known in the art can be used to verify the nucleotide' sequences of SEQ ID NO:X.. [081] The predicted amino acid sequence can then be verified from such deposits. Moreover, the amino acid sequence of the protein encoded by a particular clone can also be directly determined by peptide sequencing or by expressing the protein in a suitable host cell. containing the deposited human cDNA, collecting the protein, and determining its sequence.
  • Partial cDNA clones can be made full-length by utilizing the rapid amplification of cDNA ends (RACE) procedure described in Frohman, M.A., et al, Proc. Nat'l. Acad. Sci. USA, 85:8998-9002 (1988).
  • RACE rapid amplification of cDNA ends
  • RNA Poly A+ or- total RNA is reverse transcribed with Superscript- II (Gibco/BRL) and an antisense or complementary primer specific to the cDNA sequence.
  • the primer is removed from the reaction with a Microcon Concentrator (Amicon).
  • the first-strand cDNA is then tailed with dATP and terminal deoxynucleotide transferase (Gibco/BRL).
  • an anchor sequence is produced which is needed for PCR amplification.
  • the second strand is synthesized from the dA-tail in PCR buffer, Taq DNA polymerase (Perkin-Elmer Cetus), an oligo-dT primer containing three adjacent restriction sites (Xhol, Sail and C ) at the 5' end and a primer containing just these restriction sites.
  • This double-stranded cDNA is PCR amplified for 40 cycles with the same primers as well as a nested cDNA-specific antisense primer.
  • the PCR products are size-separated on an ethidium bromide- agarose gel and the region of gel containing cDNA products the predicted size of missing protein-coding DNA is removed.
  • cDNA is purified from the agarose with the - Magic PCR Prep kit (Promega), restriction digested with Xhol or Sail, and ligated to a plasmid such as pBluescript SKII (Stratagene) at Xhol and EcoRV sites.
  • This DNA is transformed into bacteria and. the plasmid clones sequenced to identify the correct protein-coding inserts. Correct 5' ends are confirmed by comparing this sequence with the putatively identified homologue and overlap with the partial cDNA clone. Similar methods known in the art and/or commercial kits are used to amplify and recover 3' ends.
  • kits are commercially available for purchase. Similar reagents and methods to those above are supplied in kit form from Gibco/BRL for both 5' and 3' RACE for recovery of full length genes. A second kit is available from Clontech which is a modification of a related technique, SLIC (single-stranded ligation to single-stranded cDNA), developed by Dumas et al., Nucleic Acids Res., 19:5227-32, (1991). . The major differences in procedure are that the RNA is alkaline hydrolyzed after reverse transcription and RNA ligase is used to join a restriction site-containing anchor primer to the first-strand cDNA. This obviates the necessity for the dA-tailing reaction which results in a polyT stretch that is difficult to sequence past.
  • SLIC single-stranded ligation to single-stranded cDNA
  • An alternative to generating 5' or 3' cDNA from RNA is to use cDNA library double-stranded DNA.
  • An asymmetric PCR-amplified antisense cDNA strand is synthesized with an antisense cDNA-specific primer -and a plasmid-anchored primer. These primers are removed and a symmetric PCR reaction is performed with a nested cDNA-specific antisense primer and the plasmid-anchored primer.
  • RNA oligonucleotide is ligated to the 5' ends of a population of RNA presumably containing full-length gene RNA transcript.
  • a primer set containing a primer specific to the ligated RNA oligonucleotide and a primer specific to a known sequence of the gene of interest is used to PCR amplify the 5' portion of the desired full length gene which may then be sequenced and used to generate the full length gene.
  • This method starts with total RNA isolated from the desired source, poly A RNA may be used but is not a prerequisite for this procedure.
  • RNA preparation may then be treated with phosphatase if necessary to eliminate 5' phosphate groups on degraded or damaged RNA which may interfere with the later RNA ligase step.
  • the phosphatase if used, is then inactivated and the RNA is treated with tobacco acid pyrophosphatase in order to remove the cap structure present at the 5' ends of messenger RNAs.
  • This reaction leaves a 5' phosphate group at the 5' end of the cap cleaved RNA which can then be ligated to an RNA oligonucleotide using T4 RNA ligase.
  • This modified RNA preparation can then be used as a template for first strand cDNA synthesis using a gene specific oligonucleotide.
  • the first strand synthesis reaction can then be used as a template for PCR amplification of the desired 5' end using a primer specific to the ligated RNA oligonucleotide and a primer specific to the known. sequence of the digestive system antigen of interest. The resultant product is then sequenced and analyzed to confirm that the 5' end sequence belongs to the relevant digestive system antigen.
  • the present invention also relates to vectors or plasmids, which include such
  • the material deposited with the ATCC (deposited with the ATCC on October 5, 2000, and receiving ATCC designation numbers PTA 2574 and PTA 2575; deposited with the ATCC on January 5,.2001, having the depositor reference numbers TS-1, TS-2, AC-1, and AC-2; and/or as set forth, for example, in Table 1A, 6 and 7) is a mixture of cDNA clones derived from a variety of human tissue and cloned in either a plasmid vector or a phage vector, as shown, for example, in Table 7. These deposits are referred to as "the deposits" herein.
  • the tissues from which some of the clones were derived are listed in Table 7, and the vector in which the corresponding cDNA is contained is also indicated in Table 7.
  • the deposited material includes cDNA clones corresponding to SEQ ID NO:X described, for example, in Table 1A (Clone ID NO:Z).
  • a clone which is isolatable from the ATCC Deposits by use of a sequence listed as SEQ ID NO:X may include the entire coding region of a human gene or in other cases such clone may include a substantial portion of the coding region of a human gene.
  • sequence listing may in some instances list only a portion of the DNA sequence in a clone mcluded in the ATCC Deposits, it is well within the ability of one skilled in the art to sequence the DNA mcluded in a clone contained in the ATCC Deposits by use of a sequence (or portion thereof) described in, for example Tables 1 A or 2 by procedures hereinafter further described, and others apparent to those skilled in the art.
  • Table 7 Also provided in Table 7 is the name of the vector which contains the cDNA clone. Each vector is routinely used in the art. The following additional information is provided for convenience.
  • Phagemid pBS contains an ampicillin resistance gene and pBK contains a • neomycin resistance gene.
  • Phagemid pBS may be excised from the Lambda Zap and Uni-Zap XR vectors, and phagemid pBK may be excised from the Zap Express vector. Both phagemids may be transformed into E. coli strain XL-1 Blue, also available from Stratagene.
  • Vectors pSportl, pCMVSport 1.0, pCMVSport 2.0 and pCMVSport 3.0 were obtained from Life Technologies, Inc., P: O. Box 6009, Gaithersburg, MD 20897. All Sport vectors contain an ampicillin resistance gene and may be transformed into E. coli strain DH10B, also available from Life Technologies. See, for instance, Gruber, ; C. E., et al., Focus 15:59- (1993). Vector lafmid BA (Bento Soares, Columbia University, New York, NY) contains an ampicillin resistance gene and can be transformed into E. coli strain XL-1 Blue.
  • Vector pCR ® 2.1 which is available from Invitrogen, 1600 Faraday Avenue, Carlsbad, CA 92008, contains an ampicillin resistance gene and may be transformed into E. coli strain DH10B, available from Life Technologies. See, for instance, Clark, J. M., Nuc. Acids Res. 16:9677-9686 (1988) and Mead, D. et al., Bio/Technology 9: (1991). [090] The present mvention also relates to the genes corresponding to SEQ ID NO:X,
  • SEQ ID NO:Y SEQ ID NO:Y
  • the deposited clone Clone ID NO:Z
  • the corresponding gene can be isolated in accordance with known methods using the sequence information disclosed herein. Such methods include preparing probes or primers from the disclosed sequence and identifying or amplifying the corresponding gene from appropriate sources of genomic material.
  • allelic variants, orthologs, and/or species homologs are also provided in the present invention. Procedures known in the art can be used to obtain full-length genes, allelic variants, splice variants, full-length coding portions, orthologs, and/or species homologs of digestive system associated genes corresponding to SEQ ID NO:X or the complement thereof, polypeptides encoded by SEQ ID NO:X or the complement thereof, and/or the cDNA contained in Clone ID NO:Z, using information from the sequences disclosed herein or the clones deposited with the ATCC.
  • allelic variants and/or species homologs may be isolated and identified by making suitable probes or primers from the sequences provided herein and screening a suitable nucleic acid source for allelic variants and/or the desired homologue.
  • polypeptides of the mvention can be prepared in any suitable manner.
  • polypeptides include isolated naturally occurring polypeptides, recombinantly produced polypeptides, synthetically produced polypeptides, or polypeptides produced by a combination of these methods. Means for preparing such polypeptides are well understood in the art.
  • polypeptides may be in the form of the secreted protein, including the mature form, or may be a part of a larger protein, such as a fusion protein (see below). It is often advantageous to include an additional amino acid sequence which contains secretory or leader sequences, pro-sequences, sequences which aid in purification, such as multiple histidine residues, or an additional sequence for stability during recombinant production.
  • polypeptides of the present invention are preferably provided in an isolated form, and preferably are ' substantially purified.
  • a recombinantly produced version of a polypeptide, including the secreted polypeptide can be substantially purified using techniques described herein or otherwise known in the art, such as, for example, by the one-step method described in Smith and Johnson, Gene 67:31-40 (1988).
  • Polypeptides of the mvention also can be purified from natural, synthetic or recombinant sources using techniques described herein or otherwise known in the art, such as, for example, antibodies of the invention raised against the digestive system polypeptides of the present invention in methods which are well known in the art.
  • the present mvention provides a polynucleotide comprising, or alternatively consisting of, the nucleic acid sequence of SEQ ID NO:X, and/or the cDNA sequence contained in Clone ID NO:Z.
  • the present mvention also provides a polypeptide comprising, or alternatively, consisting of, the polypeptide sequence of SEQ ID NO:Y, a polypeptide encoded by SEQ ID NO:X or a complement thereof, a polypeptide encoded by the cDNA contained in Clone ID NO:Z, and/or the polypeptide sequence encoded by a nucleotide sequence in SEQ ID NO:B as defined in column 6 of Table IB.
  • Polynucleotides encoding a polypeptide comprising, or alternatively consisting of the polypeptide sequence of SEQ ID NO:Y, a polypeptide encoded by SEQ ID NO:X, a polypeptide encoded by the cDNA contained in Clone ID NO:Z and/or a polypeptide sequence encoded by a nucleotide sequence in SEQ ID NO:B as defined in column 6 of Table IB are also encompassed by the invention.
  • the present invention further encompasses a polynucleotide comprising, or alternatively consisting of, the complement of the nucleic acid sequence of SEQ ID NO:X, a nucleic acid sequence encoding a polypeptide encoded by the complement of the nucleic acid sequence of SEQ ID NO:X, and/or the cDNA contained in Clone ID NO:Z.
  • representative examples of polynucleotides of the mvention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the sequences delineated in Table IB column 6, or any combination .thereof. Additional, representative examples of polynucleotides of the mvention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the complementary strand(s) of the sequences delineated in Table IB column 6, or any combination thereof.
  • the above-described polynucleotides of the mvention comprise, or alternatively consist of, sequences delineated in Table IB, column 6, and have a nucleic acid sequence which is different from that of the BAC fragment having the sequence disclosed in SEQ ID NO:B (see Table IB, column 5).
  • the above-described polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in Table IB, column 6, and have a nucleic acid sequence which is different from that published for the BAC clone identified as BAC ID NO: A (see Table IB, column 4).
  • the above-described polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in Table IB, column 6, and have a nucleic acid sequence which is different from that contained in the BAC clone identified as BAC ID NO:A (see Table IB, column 4).
  • Polypeptides encoded by these polynucleotides, other polynucleotides that encode these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention. Additionally, • fragments and variants of the above-described polynucleotides and polypeptides are also encompassed by the invention.
  • representative examples of polynucleotides of the mvention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the sequences delineated in column 6 of Table IB which correspond to the same Clone ID NO:Z (see Table IB, column 1), or any combination thereof.
  • Additional, representative examples of polynucleotides of the invention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the complementary strand(s) of the sequences delineated in column 6 of Table IB which correspond to the same Clone ID NO:Z (see Table IB, column 1), or any combination thereof.
  • the above-described polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in column 6 of Table IB which correspond to the same Clone ID NO:Z (see Table IB, column 1) and have a nucleic acid sequence which is different from that of the BNC fragment having the sequence disclosed in SEQ ID ⁇ O:B (see Table IB, column 5).
  • polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in column 6 of Table IB which correspond to the same Clone ID NO:Z (see Table IB, column 1) and have a nucleic acid sequence which is different from that published for the BAC clone identified as BAC ID NO:A (see Table IB, column 4).
  • the above-described polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in column 6 of Table IB which correspond to the same Clone ID NO:Z (see Table IB, column 1) and have a nucleic acid sequence which is different from that contained in the BAC clone identified as BAC ID NO:A (see Table IB, column 4).
  • Polypeptides encoded by these polynucleotides, other polynucleotides that encode these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention. Additionally, fragments and variants of the above- described polynucleotides and polypeptides are also encompassed by the invention.
  • polynucleotides of the invention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the sequences delineated in column 6 of Table IB which correspond to the same contig sequence identifer SEQ ID NO:X (see Table IB, column 2), or any combination thereof.
  • polynucleotides of the invention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the complementary strand(s) of the sequences delineated in column 6 of Table IB which correspond to the same contig sequence identifer SEQ ID NO:X (see Table IB, column 2), or any combination thereof.
  • the above-described polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in column 6 of Table IB which correspond to the same contig sequence identifer SEQ ID NO:X (see Table IB, column 2) and have a nucleic acid sequence which is different from that of the BAC fragment having the sequence disclosed in SEQ ID NO:B (see Table IB, column 5).
  • the above-described polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in column 6 of Table IB which correspond to the same contig sequence identifer SEQ ID NO:X (see Table IB, column 2) and have a nucleic acid .
  • polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in column 6 of Table IB which correspond to the same contig sequence identifer SEQ ID NO:X (see Table IB, column 2) and have a nucleic acid sequence which is different from that contained in the BAC clone identified as BAC ID NO: A (See Table IB, column 4).
  • Polypeptides encoded by these polynucleotides, other polynucleotides that encode these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention.
  • polynucleotides of the invention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the sequences delineated in the same row of Table IB column 6, or any combination thereof.
  • representative examples of polynucleotides of the invention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the complementary strand(s) of the sequences delineated in the same row of Table IB column 6, or any combination thereof.
  • the polynucleotides of the invention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the complementary strand(s) of the sequences delineated in the same row of Table IB column 6, wherein sequentially delineated sequences in the table (i.e. corresponding to those exons located closest to each other) are directly contiguous in a 5' to 3' orientation.
  • above-described polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in the same row of Table IB, column 6, and have a nucleic acid sequence which is different from that of the BAC fragment having the sequence disclosed in SEQ ID NO:B (see Table IB, column 5).
  • the above-described polynucleotides of the invention comprise, or alternatively consist of, sequences delineated in the same row of Table IB, column 6, and have a nucleic acid sequence which is different from that published for the BAC clone identified as BAC ID NO:A (see Table IB, column 4).
  • polynucleotides of the mvention comprise, or alternatively consist of, sequences delineated in the same row of Table IB, column 6, and have a nucleic acid sequence which is different from that contained in the BAC clone identified as BAC ID NO:A (see Table IB, column 4).
  • Polypeptides encoded by these polynucleotides, other polynucleotides that encode these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention.
  • polynucleotides of the invention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the sequences delineated in column 6 of Table IB, and the polynucleotide sequence of SEQ ID NO:X (e.g., as defined in Table IB, column 2) or fragments or variants thereof.
  • Polypeptides encoded by these polynucleotides, other polynucleotides that encode these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention.
  • polynucleotides of the mvention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the sequences delineated in column 6 of Table IB which correspond to the same Clone ID NO:Z (see Table IB, column 1), and the polynucleotide sequence of SEQ ID NO:X (e.g., as defined in Table 1 A or IB) or fragments or variants thereof.
  • the delineated sequence(s) and polynucleotide sequence of SEQ ID NO:X correspond to the same Clone ID NO:Z.
  • Polypeptides encoded by these polynucleotides, other polynucleotides that encode these polypeptides, and antibodies that bind these polypeptides are also encompassed by the mvention.
  • polynucleotides of the invention comprise, or alternatively consist of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the sequences delineated in the same row of column 6 of Table IB, and the polynucleotide sequence of SEQ ID NO:X (e.g., as defined in Table 1 A or IB) or fragments or variants thereof.
  • the delineated sequence(s) and polynucleotide sequence of SEQ ID NO:X correspond to the same row of column 6 of Table IB.
  • Polypeptides encoded by these polynucleotides, other polynucleotides that encode these polypeptides, and antibodies that bind these polypeptides are also encompassed by the mvention.
  • polynucleotides of the invention comprise, or alternatively consist of a polynucleotide sequence in which the 3' 10 polynucleotides of one of the sequences delineated in column 6 of Table IB and the 5' 10 polynucleotides of the sequence of SEQ ID NO:X are directly contiguous. Nucleic acids which hybridize to the complement of these 20 contiguous polynucleotides under stringent hybridization conditions or alternatively, under lower stringency conditions, are also encompassed by the invention.
  • Polypeptides encoded by these polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic acids that encode these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention. Additionally, fragments and variants of the above- described polynucleotides, nucleic acids, and polypeptides are also encompassed by the invention.
  • polynucleotides of the mvention comprise, or alternatively consist of, a polynucleotide sequence in which the 3' 10 polynucleotides of one of the sequences delineated in column 6 of Table IB and the 5' 10 polynucleotides of a fragment or variant of the sequence of SEQ ID NO:X are directly contiguous Nucleic acids which hybridize to the complement of these 20 contiguous polynucleotides under stringent hybridization conditions or alternatively, under lower stringency conditions, are also encompassed by the invention.
  • Polypeptides encoded by these polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic acids encodmg these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention. Additionally, fragments and variants of the above-described polynucleotides, nucleic acids, and polypeptides are also encompassed by the invention.
  • polynucleotides of the invention comprise, or alternatively consist of, a polynucleotide sequence in which the 3' 10 polynucleotides of the sequence of SEQ ID NO:X and the 5' 10 polynucleotides of the sequence of one of the sequences delineated in column 6 of Table IB are directly contiguous. Nucleic acids which hybridize to the complement of these 20 contiguous polynucleotides under stringent hybridization conditions or alternatively, under lower stringency conditions, are also encompassed by the mvention.
  • Polypeptides encoded by these polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic acids encoding these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention. Additionally, fragments and variants of the above- described polynucleotides, nucleic acids, and polypeptides are also encompassed by the invention.
  • polynucleotides of the invention comprise, or alternatively consist of, a polynucleotide sequence in which the 3' 10 polynucleotides of a fragment or variant of the sequence of SEQ ID NO:X and the 5' 10 polynucleotides of the sequence of one of the sequences delineated in column 6 of Table IB are directly contiguous. Nucleic acids which hybridize to the complement of these 20 contiguous polynucleotides under stringent hybridization conditions or alternatively, under lower stringency conditions, are also encompassed by the invention.
  • Polypeptides encoded by these polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic acids encoding these polypeptides, and antibodies that bind these polypeptides are also encompassed by the mvention. Additionally, fragments and variants of the above-described polynucleotides, nucleic acids, and polypeptides, are also encompassed by the invention. -
  • polynucleotides of the invention comprise, or alternatively consist of, a polynucleotide sequence in which the 3' 10 polynucleotides of one of the sequences delineated in column 6 of Table IB and the 5' 10 polynucleotides of another sequence in column 6 are directly contiguous. Nucleic acids which hybridize to the complement of these 20 contiguous polynucleotides under stringent hybridization conditions or alternatively, under lower stringency conditions, are also encompassed by the invention.
  • Polypeptides encoded by these polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic acids encoding these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention. Additionally, fragments and variants of the above- described polynucleotides, nucleic acids, and polypeptides are also encompassed by the invention.
  • polynucleotides of the mvention comprise, or alternatively consist of, a polynucleotide sequence in which the 3' 10 polynucleotides of one of the sequences delineated in column 6 of Table IB and the 5' 10 polynucleotides of another sequence in column 6 corresponding to the same Clone ID NO:Z (see Table IB, column 1) are directly contiguous. Nucleic acids which hybridize to the complement of these 20 lower stringency conditions, are also encompassed by the invention.
  • Polypeptides encoded by these polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic acids encodmg these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention. Additionally, fragments and variants of the above-described polynucleotides, nucleic acids, and polypeptides are also encompassed by the invention.
  • polynucleotides of the invention comprise, or alternatively consist of, a polynucleotide sequence in which the 3 ' 10 polynucleotides of one sequence in column 6 corresponding to the same contig sequence identifer SEQ ID NO:X (see Table IB, column 2) are directly contiguous. Nucleic acids which hybridize to the complement of these 20 contiguous polynucleotides under stringent hybridization conditions or alternatively, under lower stringency conditions, are also encompassed by the invention.
  • Polypeptides encoded by these polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic acids encodmg these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention. Additionally, fragments and variants of the above-described polynucleotides, nucleic acids, and polypeptides are also encompassed by the invention.
  • polynucleotides of the mvention comprise, or alternatively consist of a polynucleotide sequence in which the 3' 10 polynucleotides of one of the sequences delineated in column 6 of Table IB and the 5' 10 polynucleotides of another sequence in column 6 corresponding to the same row are directly contiguous.
  • the 3' 10 polynucleotides of one of the sequences delineated in column 6 of Table IB is directly contiguous with the 5' 10 polynucleotides of the next sequential exon delineated in Table IB, column 6.
  • Nucleic acids which hybridize to the complement of these 20 contiguous polynucleotides under stringent hybridization conditions or alternatively, under lower stringency conditions are also encompassed by the invention.
  • Polypeptides encoded by these polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic acids encodmg these polypeptides, and antibodies that bind these polypeptides are also encompassed by the invention. Additionally, fragments and variants of the above- described polynucleotides, nucleic acids, and polypeptides are also encompassed by the invention.
  • polynucleotide sequences such as EST sequences, are publicly available and accessible through sequence databases and may have been publicly available prior to conception of the present invention. Preferably, such related polynucleotides are specifically excluded from the scope of the present invention.
  • each contig sequence (SEQ ID NO:X) listed in the third column of Table 1A preferably excluded are one or more polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a is any integer between 1 and the final nucleotide minus 15 of SEQ ID NO:X, b is an integer of 15 to the final nucleotide of SEQ ID NO:X, where both a and b correspond to the positions of nucleotide residues shown in SEQ ID NO:X, and where b is greater than or equal to a + 14.
  • polynucleotides comprising a nucleotide sequence described by the general formula of a-b, where a and b are integers as defined in columns 4 and 5, respectively, of Table 3.
  • the polynucleotides of the mvention do not consist of at least one, two, three, four, five, ten, or more of the specific polynucleotide sequences referenced by the Genbank Accession No. as disclosed in column 6 of Table 3(including for example, published sequence in connection with a particular BAC clone).
  • preferably excluded from the invention are the specific polynucleotide sequence(s) contained in the clones corresponding to at least one, two, three, four, five, ten, or more of the available material having the accession numbers identified in the sixth column of this Table (including for example, the actual sequence contained in an identified BAC clone). In no way is this listing meant to encompass all of the sequences which may be excluded by the general formula, it is just a representative example. All references available through these accessions are hereby incorporated by reference in their entirety.
  • AI432229 AI500659, AI799199, AI349226, AW235035, AI934036, AI889203, AI754897, AI345744, AI580984, AI680113, AI862142, AI874109, AI889839, AW078529, AW301300, AI349598, AI273142, A 075351, AI628205, AI597918, AI539153, AL042753, AI921379, AL120854, AI609592, AI859733, AI583316, AI492540, AI802542, AI282903, AW026882, AW166645, AW167776, AI610756, AW080838, AI445165, AL040169, AI872711, AW129202, AI432969, AW169671, AL044207, AW118512, AW196141, AW104724, AI334902, AI804585, AI696398, AI609580, A 302992,
  • AW068316 AA608751, AA639946, T54275, AA621838, AI266003, AI753113, AI054333, W42997, AI358928, AI361063, AI525532, AI354847, AJ230815, AA573207, AA702326, AI369977, H86105, AA618035, T71936, AW340905, AW070900, AA486785, AA559023, AW407473, AI355414, AW022734, D29168, H53169, AA228442, AA584594, N23229, AA292227, AA399158, AW275763, AA633920, AA515905, AA298531, AA094109, AA508509, AI925579, AI828331, H68563, AA483599, AA225652, AI801771, AW247866, R86240, Z99364,
  • HVAAE01 518 915732 1 - 515 15 - 529 AI819354, AI560690, AI393635, AI580846, AI024796, AI242427, AI393644, A 020098, R40205, AA568464, F08882, AI190763, AA121140, AA059294, H72102, H92545, N74993,
  • HVAAE94 519 968675 1 - 332 15 - 346 AA844907, AA845137, and AA367039.
  • AW303196 AA521399, AA521323, AA623002, AW274349, AA847499, AW301350, AW439558, AI076616, AI350211, AA493708, AW270382, AW021583, AA525824, AI345518, AA584201, AI754658, H71429, AI499938, AL042753, AA533036, AA126450, AA613232, AA984708, AW274346, AA682912, AA719292, AI110770, AA503473, AA502104, AA528516, AA483771, AI110760, AW072923, AL042420, AI568678, AA584167, AA632837, AA631507, AI246119, AI434695, AI732120, AW080811, AE54615, AA394271, AI860013, AI133164, AA613227,
  • AL041142 AL040332, AL045990, AL041197, AL044199, AL040529, AL040571, AL039643, AL046330, AL041277, AL079878, AL039338, AL040745, AL040370, AL040128, AL047036, AL044274, AL040553, AL040342, AL041186, AL040155, AL040414, AL040285, AL039744, AL040091, AL039432, AL044165, AL042096, AL041131, AL037341, AL043941, AL040090, AL045989, AL041051, AL040168, AL044201, AL046327, AI547295, AL043775, AL043444, AL045327, AL040253, AL041227, AL045857, AL040082, AL040329, AL037279, AL047037, AL041278, AL040238, AL040263, AL041140,
  • HWMEI07 643 830227 1 - 302 15 - 316 AW148716, AI917055, N42321, AL038605, AI802542, AW302965, AI815855, AI340603, AA427700, AI308032,
  • HVASJ79 765 951617 1 - 1632 15 - 1646 AA873275, AI830154, AI079818, AI361958, AW302989,
  • AI668606 AI000192, AI873854, AW021774, AA731723, AA181513, AA152416, AI591299, AI590522, AA994578, AI344810, AI916335, AA176836, AW302048, AL045077, AA523820, AA505070, AI525532, AA441878, AA446723, AI433247, AI284583, AI590459, AW339622, N22032, AW022317, AI075935, AI826845, AA125988, R02089, AW082744, AL021938, AC007051, Z85987, AF111168, AC004448, AP000557, AC005081, AC002400, AC006064, AC005015, AP000552, AC006312, AC005899, AC005747, AL022313, AL008582, AC002115, AL031005,
  • HLQIF28 970 856619 1 - 372 15 - 386 T64673, T74667, T58830, AL121739, AB024079, AL021879, and AF104312.
  • AA605030 D51927, AA487829, AA467997, AA665517, AA658554, AA635413, AI061303, AI469468, AA847982, AA346436, AA487720, T92237, AL047645, AA653955, AA411741, W39287, W24312, AA482792, W60522, AA856904, AA445951, AI885465, AA593828, AA630854, AI671077, AA427808, AA780906, AI627917, AI281622, AA604515, AI583745, AI049955, R99613, AI733660, AA165079, AA420546, AA725642, AA161141, AI668566, AI821775, AA496369, AI754719, AA665475, AW243945, AI624781, AA192346, R174
  • HGBHD89 1142 493910 1 - 538 15 - 552 AI187148, AW272389, AA565547, AW069227, AW328446, AI815210, AW069769, AI573198, AI278440, AI277373, AI306624, AI038304, AI421666, AI567676, AA809116, AI634187, AI755214, AI754567, AA514450, AA857673, AI291439, AI457313, AW148775, AI537995, AI733523, AI754105, AW168846, AA525517, T47138, AW303008, AI797998, AI130709, AI733856, AI814682, AI150934, AI732251, AA809546, T57096, AI732911, AI431513, AA491814, AI080307, AA834816, AI243793, AW401509, AI338899,
  • LO AW162071, AI434468, AW151485, AW129659, AI312428, Y11587, 148979, 148978, AF090900, 189947, AF078844, A08916, A08913, AF113019, AL110196, AF090903, AL117460, AF113677, AR011880, X84990, 189931, AL050393, AL133640, AF177401, 149625, AL049314, AL133080, E02349, AF111851, AL049466, AF113689, AL117457, AL050116, AF090934, A08910, AL050149, AL080060, AF090901, X82434, AL110221, AF118070, AL122121, Y16645, S78214, AL133075, AF106862, E07361, Y11254, AL133560, ALI 17585, AL133565, A
  • the present invention is also directed to variants of the digestive system associated polynucleotide sequence disclosed in SEQ ID NO:X or the complementary strand thereto, nucleotide sequences encoding the polypeptide of SEQ ID NO:Y, the nucleotide sequence of SEQ ID NO:X encoding the polypeptide sequence as defined in column 6 of Table 1A, nucleotide sequences encoding the polypeptide as defined in column 6 of Table 1 A, the nucleotide sequence as defined in columns 8 and 9 of Table 2, nucleotide sequences encoding the polypeptide encoded by the nucleotide sequence as defined in columns 8 and 9 of Table 2, the nucleotide sequence as defined in column 6 of Table IB, nucleotide sequences encoding the polypeptide encoded by the nucleotide sequence as defined in column 6 of Table IB, the cDNA sequence contained in Clone ID NO:Z, and/or nucleotide sequences encoding a polypeptide encode
  • the present invention also encompasses variants of the polypeptide sequence disclosed in SEQ ID NO:Y, a polypeptide sequence as defined in column 6 of Table 1A, a polypeptide sequence encoded by the polynucleotide sequence in SEQ ID NO:X, a polypeptide sequence encoded by the nucleotide sequence as defined in columns 8 and 9 of Table 2, a polypeptide sequence encoded by the nucleotide sequence as defined in column 6 of Table IB, a polypeptide sequence encoded by the complement of the polynucleotide sequence in SEQ ID NO:X, and/or a polypeptide sequence encoded by the cDNA sequence contained in Clone ID NO :Z.
  • Variant refers to a polynucleotide or polypeptide differing from. the polynucleotide or polypeptide of the present mvention, but retaining essential properties thereof. Generally, variants are overall closely similar, and, in many regions, identical to the polynucleotide or polypeptide of the present invention.
  • one aspect of the invention provides an isolated nucleic acid molecule comprising, or alternatively consisting of, a polynucleotide having a nucleotide sequence selected from the group consisting of: (a) a nucleotide sequence described in SEQ ID NO:X or contained in the cDNA sequence of Clone ID NO:Z; (b) a nucleotide sequence in SEQ ID NO:X or the cDNA in Clone ID NO:Z which encodes a mature digestive system associated polypeptide; (c).
  • nucleotide sequence in SEQ ID NO:X or the cDNA sequence of Clone ID NO:Z which encodes a biologically active fragment of a digestive system associated polypeptide
  • a nucleotide sequence in SEQ ID NO:X or the cDNA sequence of Clone ID NO:Z which encodes an antigenic fragment of a digestive system associated polypeptide
  • the present invention is also directed to nucleic acid molecules which comprise, or alternatively consist of, a nucleotide sequence which is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100%, identical to, for example, any of the nucleotide sequences in (a), (b), (c), (d), (e), .(f), (g), (h), or (i) above, the nucleotide coding sequence in SEQ ID NO:X or the complementary strand thereto, the nucleotide coding sequence of the cDNA contained in Clone ID NO:Z or the complementary strand thereto, a nucleotide sequence encoding the polypeptide of SEQ ID NO:Y, a nucleotide sequence encoding a polypeptide sequence encoded by the nucleotide sequence in SEQ ID NO:X, a polypeptide sequence encoded by the complement of the polynucleotide sequence in SEQ ID NO:X, a nucleo
  • Polynucleotides which hybridize to the complement of these nucleic acid molecules under stringent hybridization conditions or alternatively, under lower stringency conditions, are also encompassed by the mvention, as are polypeptides encoded by these polynucleotides and nucleic acids.
  • the invention encompasses nucleic acid molecules which comprise, or alternatively, consist of a polynucleotide which hybridizes under stringent hybridization conditions, or alternatively, under lower stringency conditions, to a polynucleotide in (a), (b), (c), (d), (e), (f), (g), (h), or (i) above, as are polypeptides encoded by these polynucleotides.
  • polynucleotides which hybridize to the complement of these nucleic acid molecules under stringent hybridization conditions or alternatively, under lower stringency conditions are also encompassed by the invention, as are polypeptides encoded by these polynucleotides.
  • the mvention provides a purified protein comprising, or alternatively consisting of, a polypeptide having an amino acid sequence selected from the group consisting of: (a) the complete amino acid sequence of SEQ ID NON or the complete amino acid sequence encoded by the cD ⁇ A in Clone ID ⁇ O:Z; (b) the amino acid sequence of a mature digestive system associated polypeptide having the amino acid sequence of SEQ ID NO:Y or the amino acid sequence encoded by the cDNA in Clone ID NO:Z; (c) the amino acid sequence of a biologically active fragment of a digestive system associated polypeptide having the complete amino acid sequence of SEQ ID NO:Y or the complete amino acid sequence encoded by the cDNA in Clone ID NO/.Z; and (d) the amino acid sequence of an antigenic fragment of a digestive system associated polypeptide having the complete amino acid sequence of SEQ ID NO:Y or the complete amino acid sequence encoded by the cDNA in Clone ID NO:Z.
  • the present invention is also directed to proteins which comprise, or alternatively consist of, an amino acid sequence which is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100%, identical to, for example, any of the amino acid sequences in (a), (b), (c), or (d), above, the amino acid sequence shown in SEQ ID NO:Y, the amino acid sequence encoded by the cDNA contained in Clone ID NO:Z, the amino acid sequence of the polypeptide encoded by the nucleotide sequence in SEQ ID NO:X as defined in columns 8 and 9 of Table 2, the amino acid sequence of the polypeptide encoded by the nucleotide sequence in SEQ ID NO:B as defined in column 6 of Table IB, the amino acid sequence as defined in column 6 of Table 1A, an amino acid sequence encoded by the nucleotide sequence in SEQ ID NO:X, and an amino acid sequence encoded by the complement of the polynucleotide sequence in SEQ ID NO:X.
  • polypeptides are also provided (e.g., those fragments described herein).
  • Further proteins encoded by polynucleotides which hybridize to the complement of the nucleic acid molecules encodmg these amino acid sequences under stringent hybridization conditions or alternatively, under lower stringency conditions, are also encompassed by the invention, as are the polynucleotides encoding these proteins.
  • nucleotide sequence of the nucleic acid is identical to the reference sequence except that the nucleotide sequence may include up to five point mutations per each 100 nucleotides of the reference nucleotide sequence encoding the polypeptide.
  • nucleotide sequence may include up to five point mutations per each 100 nucleotides of the reference nucleotide sequence encoding the polypeptide.
  • nucleic acid having a nucleotide sequence at least 95% identical to a reference nucleotide sequence up to 5% of the nucleotides in the reference sequence may be deleted or substituted with another nucleotide, or a number of nucleotides up to 5% of the total nucleotides in the reference sequence may be inserted into the reference sequence.
  • the query sequence may be an entire sequence referred to in Table 1A or 2 as the ORF (open reading frame), or any fragment specified, as described herein.
  • nucleotide sequence of the present invention can be determined conventionally using known computer programs.
  • a preferred method for determining the best overall match between a query sequence (a sequence of the present invention) and a subject sequence, also referred to as a global sequence alignment can be determined using the FASTDB computer program based on the algorithm of Brutlag et al. (Comp. App. Biosci. 6:237-245 (1990)).
  • the query and subject sequences are both DNA sequences.
  • RNA sequence can be compared by converting U's to T's.
  • the result of said global sequence alignment is expressed as percent identity.
  • This percentage is then subtracted from the percent identity, calculated by the above FASTDB program using the specified parameters, to arrive at a final percent identity score.
  • This corrected score is what is used for the purposes of the present invention. Only bases outside the 5' and 3' bases of the subject sequence, as displayed by the FASTDB alignment, which are not matched/aligned with the query sequence, are calculated for the purposes- of manually adjusting the percent identity score.
  • a 90 base subject sequence is aligned to a 100 base query sequence to determine percent identity.
  • the deletions occur at the 5' end of the subject sequence and therefore, the FASTDB alignment does not show a matched/alignment of the first 10 bases at 5' end.
  • the 10 unpaired bases represent 10%» of the sequence (number of bases at the 5' and 3' ends not matched/total number of bases in the query sequence) so 10% is subtracted from the percent identity score calculated by the FASTDB program. If the remaining 90 bases were perfectly matched the final percent identity would be 90%.
  • a 90 base subject sequence is compared with a 100 base query sequence.
  • deletions are internal deletions so that there are no bases on the 5' or 3' of the subject sequence which are not matched/aligned with the query.
  • percent identity calculated by FASTDB is not manually corrected.
  • bases 5' and 3' of the subject sequence which are not matched/aligned with the query sequence are manually corrected for. No other manual corrections are to made for the purposes of the present invention.
  • polypeptide having an amino acid sequence at least, for example, 95%
  • amino acid sequence of the subject polypeptide is identical to the query sequence except that the subject polypeptide sequence may include up to five amino acid alterations per each 100 amino acids of the query amino acid -sequence.
  • up to 5% of the amino acid residues in the subject sequence may be inserted, deleted, (indels) or substituted with another amino acid.
  • These alterations of the reference sequence may occur at the amino or carboxy terminal positions of the reference amino acid sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence.
  • amino acid sequence of the polypeptide encoded by the polynucleotide sequence in SEQ ID NO:B as defined in column 6 of Table IB or a fragment thereof, the amino acid sequence of the polypeptide encoded by the nucleotide sequence in SEQ ID NO:X or a fragment thereof, or an amino acid sequence of the polypeptide encoded by cDNA contained in Clone ID NO:Z, or a fragment thereof, can be determined conventionally using known computer programs.
  • a sequence of the present invention and a subject sequence can be determined using the FASTDB computer program based on the algorithm of Brutlag et al. (Comp. App. Biosci.6:237-245 (1990)).
  • the query and subject sequences are either both nucleotide sequences or both amino acid sequences.
  • the result of said global sequence alignment is expressed as percent identity.
  • the percent identity is corrected by calculating the number of residues of the query sequence that are N- and C-terminal of the subject sequence, which are not matched/aligned with a corresponding subject residue, as a percent of the total bases of the query sequence. Whether a residue is matched/aligned is determined by results of the FASTDB sequence alignment.
  • This percentage is then subtracted from the percent identity, calculated by the above FASTDB program using the specified parameters, to arrive at a final percent identity score.
  • This final percent identity score is what is used for the purposes of the present mvention. Only residues to the N- and C-termini of the subject sequence, which are not matched/aligned with the query sequence, are considered for the purposes of manually adjusting the percent identity score. That is, only query residue positions outside the farthest N- and C- terminal residues of the subject sequence.
  • a 90 amino acid residue subject sequence is aligned with a
  • deletion occurs at the N-terminus of the subject sequence and therefore, the FASTDB alignment does not show a matching/alignment of the first 10 residues at the N-terminus.
  • the 10 unpaired residues represent 10% of the sequence (number of residues at the N- and C- termini not matched/total number of residues in the query sequence) so 10% is subtracted from the percent identity score calculated by the FASTDB program. If the remaining 90 residues were perfectly matched the final percent identity would be 90%.
  • a 90 residue subject sequence is compared with a 100 residue query sequence. This time the deletions are internal deletions so there are no residues at the N- or C-termini of the subject sequence which are not matched/aligned with the query.
  • the polynucleotide variants of the invention may contain alterations in the coding regions, non-coding regions, or both. Especially preferred are polynucleotide variants containing alterations which produce silent substitutions, additions, or deletions, but do not alter the properties or activities of the encoded polypeptide. Nucleotide variants produced by silent substitutions due to the degeneracy of the genetic code are preferred. Moreover, polypeptide variants in which less than 50, less . than 40, less than 30, less than 20, less than 10, or 5-50, 5-25, 5-10, 1-5, or 1-2 amino acids are substituted, deleted, or added in any combination are also preferred. Polynucleotide variants can be produced for a variety of reasons, e.g., to optimize codon expression for a particular host (change codons in the human mRNA to those preferred by a bacterial host such as E. coli).
  • Naturally occurring variants are called "allelic variants,” and refer to one of
  • allelic variants can vary at either the polynucleotide and/or polypeptide level and are included in the present mvention. Alternatively,. non-naturaUy occurring, variants may be produced by mutagenesis techniques or by direct synthesis.
  • variants may be generated to improve or alter the characteristics of the polypeptides of the present invention.
  • one or more amino acids can be deleted from the N-terminus or C-terminus of the polypeptides of the present mvention without substantial loss of biological function.
  • the authors of Ron et al., J. Biol. Chem. 268: 2984-2988 (1993) reported variant KGF proteins having heparin binding activity even after deleting 3, 8, or 27 amino-terminal amino acid residues.
  • Interferon gamma exhibited up to ten times higher activity after deleting 8-10 amino acid residues from, the carboxy terminus of this protein. (Dobeli. et al., J. Biotechnology 7:199-216 (1988). . )
  • the invention further includes polypeptide variants which show a functional activity (e.g., biological activity) of the polypeptides of the invention.
  • a functional activity e.g., biological activity
  • variants include deletions, insertions, inversions, repeats, and substitutions selected according to general rules known in the art so as have little effect on activity.
  • the present application is directed to nucleic acid molecules at least 80%,
  • nucleic acid sequences disclosed herein e.g., encoding a polypeptide having the amino acid sequence of an N and/or C terminal deletion
  • a polypeptide having functional activity e.g., a particular nucleic acid molecule does not encode a polypeptide having functional activity, one of skill in the art would still know how to use the nucleic acid molecule, for instance, as a hybridization probe or a polymerase chain reaction (PCR) primer.
  • PCR polymerase chain reaction
  • nucleic acid molecules of the present invention that do not encode a polypeptide having functional activity include, ter alia, (1) isolating a gene or allelic or splice variants thereof in a cDNA library; (2) in situ hybridization (e.g., "FISH") to metaphase chromosomal spreads to provide precise chromosomal location of the gene, as described in Verma et al., Human Chromosomes: A Manual of Basic Techniques, Pergamon Press, New York (1988); (3) Northern Blot analysis for detecting mRNA expression in specific tissues (e.g., normal digestive system or diseased digestive system tissues); and (4) in situ hybridization (e.g., histochemistry) for detecting mRNA expression in specific tissues (e.g., normal digestive system or diseased digestive system tissues).
  • in situ hybridization e.g., histochemistry
  • nucleic acid molecules having sequences at least
  • a polypeptide having functional activity is meant, a polypeptide capable of displaying one or more known functional activities associated with a full-length (complete) protein of the mvention.
  • Such functional activities include, but are not limited to, biological activity, antigenicity [ability to bind (or compete with a polypeptide of the mvention for binding) to an anti-polypeptide of the invention antibody], immunogenicity (ability to generate antibody which binds to a specific polypeptide of the invention), ability to form multimers with polypeptides of the invention, and ability to bind to a receptor or ligand for a polypeptide of the invention.
  • polypeptides, and fragments, variants and derivatives of the mvention can be assayed by various methods.
  • immunoassays known in the art can be used, including but not limited to, competitive and non-competitive assay systems using techniques such as radioimmunoassays, ELISA .(enzyme linked immunosorbent assay), "sandwich” immunoassays, immunoradiometric assays, gel diffusion precipitation reactions, immunodiffusion assays, in situ immunoassays (using colloidal gold, enzyme or radioisotope labels, for example), western blots, precipitation reactions, agglutination assays (e.g., gel agglutination assays, hemagglutination assays), complement fixation assays, immunofluorescence assays, protein A assays, and immunoelectrophoresis assays, etc.
  • competitive and non-competitive assay systems using techniques such as radioimmunoassays, ELISA .(enzyme linked immunosorbent assay), "sandwich” immunoassays, immuno
  • antibody binding is detected by detecting a label on the primary antibody.
  • the primary- antibody is detected by detecting binding of a secondary antibody or reagent to the primary antibody.
  • the secondary antibody is labeled. Many means are known in the art for detecting binding in an immunoassay and are within the scope of the present invention.
  • binding can be assayed, e.g., by means well-known in the art, such as, for example, reducing and non-reducing gel chromatography, protein affinity chromatography, and affinity blotting. See generally, Phizicky et al., Microbiol. Rev. 59:94-123 (1995).
  • the ability of physiological correlates of a polypeptide of the present invention to bind to a substrate(s) of the polypeptide of the invention can be routinely assayed using techniques known in the art.
  • nucleic acid sequence of the cDNA contained in Clone ID NO:Z having a sequence at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to, for example, the nucleic acid sequence of the cDNA contained in Clone ID NO:Z, a nucleic acid sequence referred to in Table 1A (e.g., SEQ ID NO:X), a nucleic acid sequence disclosed in Table 2 (e.g., .the nucleic acid sequence delineated in columns 8 and 9) or fragments thereof, will encode polypeptides "having functional activity.” In fact, since degenerate variants of any of these nucleotide sequences all encode the same polypeptide, in many instances, this will be clear to the skilled artisan even without performing the above described comparison assay.
  • nucleic acid molecules that are not degenerate variants, a reasonable number will also encode a polypeptide having functional activity. This is because the skilled artisan is fully aware of amino acid substitutions that are either less likely or not likely to significantly effect protein function (e.g., replacing one aliphatic amino acid with a second aliphatic amino acid), as further described below.
  • the first strategy exploits the tolerance of amino acid substitutions by natural selection during the process of evolution. By comparing amino acid sequences in different species, conserved amino acids can be identified. These conserved amino acids are likely important for protem function. In contrast, the amino acid positions where substitutions have been tolerated by natural selection indicates that these positions are not critical for protein function. Thus, positions tolerating amino acid substitution could be modified while still maintaining biological activity of the protem.
  • the second strategy uses genetic engineering to introduce amino acid changes at specific positions of a cloned gene to identify regions critical for protein function. For example, site directed mutagenesis or alanine-scanning mutagenesis (introduction of single alanine mutations at every residue in the molecule) can be used. See Cunningham et al., Science 244:1081-1085 (1989). The resulting mutant molecules can then be tested for biological activity.

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  • Peptides Or Proteins (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)

Abstract

La présente invention concerne des polynucléotides associés au système digestif et des polypeptides codant pour ces polynucléotides, appelés collectivement ici « antigènes du système digestif », ainsi que l'utilisation desdits antigènes pour la détection d'affections du système digestif, en particulier du cancer du système digestif, métastasé ou non. Plus précisément, l'invention concerne des molécules d'acide nucléique isolées associées au système digestif qui codent pour les nouveaux polypeptides associés au système digestif, ainsi que des polypeptides et anticorps du système digestif qui se lient à ces polypeptides. L'invention concerne également des vecteurs, des cellules hôtes et des méthodes synthétiques et recombinantes permettant de produire des polynucléotides et/ou des polypeptides associés au système digestif humain. Par ailleurs, l'invention concerne des méthodes diagnostiques et thérapeutiques utiles pour le diagnostic, le traitement, la prévention e/ou le pronostic de troubles du système digestif, dont le cancer, ainsi que des méthodes de traitement de tels troubles. Sont également décrites des méthodes de criblage permettant d'identifier des agonistes et des antagonistes des polynucléotides et polypeptides de l'invention, ainsi que des méthodes et/ou des compositions propres à inhiber la production et la fonction des polypeptides selon l'invention.
EP01910329A 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps Withdrawn EP1255766A2 (fr)

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PCT/US2001/001324 WO2001055314A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps

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EP1255766A2 true EP1255766A2 (fr) 2002-11-13

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EP01910325A Withdrawn EP1254219A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01910335A Withdrawn EP1254218A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01910337A Withdrawn EP1255776A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912656A Withdrawn EP1252176A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912662A Withdrawn EP1255767A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01922230A Withdrawn EP1259526A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01910329A Withdrawn EP1255766A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01914331A Withdrawn EP1254173A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01910326A Withdrawn EP1252289A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912653A Withdrawn EP1252185A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01920103A Withdrawn EP1261637A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01928288A Withdrawn EP1254147A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01926335A Withdrawn EP1263944A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912655A Withdrawn EP1261703A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et antigenes
EP01910336A Withdrawn EP1252302A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01910328A Withdrawn EP1261634A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01916068A Withdrawn EP1255817A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01910334A Withdrawn EP1259642A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01908617A Withdrawn EP1252290A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912664A Withdrawn EP1255778A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912658A Withdrawn EP1254248A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01924085A Withdrawn EP1261745A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912650A Withdrawn EP1255777A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912649A Withdrawn EP1261380A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01924081A Withdrawn EP1254153A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912657A Withdrawn EP1261618A2 (fr) 2000-01-31 2001-01-17 Acides ncleiques, proteines et anticorps
EP01912651A Withdrawn EP1252303A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01910331A Withdrawn EP1259540A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912654A Withdrawn EP1254172A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01918156A Withdrawn EP1254151A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines, et anticorps
EP01914330A Withdrawn EP1252297A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01924084A Withdrawn EP1265910A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01924086A Withdrawn EP1259531A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01910332A Withdrawn EP1255864A1 (fr) 2000-01-31 2001-01-17 Acides nucl iques, proteines et anticorps
EP01920102A Withdrawn EP1254152A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines, et anticorps
EP01908611A Withdrawn EP1261633A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912652A Withdrawn EP1254171A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01910330A Withdrawn EP1255768A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines, et anticorps

Family Applications Before (6)

Application Number Title Priority Date Filing Date
EP01910325A Withdrawn EP1254219A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01910335A Withdrawn EP1254218A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01910337A Withdrawn EP1255776A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912656A Withdrawn EP1252176A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912662A Withdrawn EP1255767A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01922230A Withdrawn EP1259526A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps

Family Applications After (31)

Application Number Title Priority Date Filing Date
EP01914331A Withdrawn EP1254173A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01910326A Withdrawn EP1252289A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912653A Withdrawn EP1252185A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01920103A Withdrawn EP1261637A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01928288A Withdrawn EP1254147A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01926335A Withdrawn EP1263944A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912655A Withdrawn EP1261703A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et antigenes
EP01910336A Withdrawn EP1252302A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01910328A Withdrawn EP1261634A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01916068A Withdrawn EP1255817A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01910334A Withdrawn EP1259642A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01908617A Withdrawn EP1252290A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912664A Withdrawn EP1255778A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912658A Withdrawn EP1254248A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01924085A Withdrawn EP1261745A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912650A Withdrawn EP1255777A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912649A Withdrawn EP1261380A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01924081A Withdrawn EP1254153A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912657A Withdrawn EP1261618A2 (fr) 2000-01-31 2001-01-17 Acides ncleiques, proteines et anticorps
EP01912651A Withdrawn EP1252303A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01910331A Withdrawn EP1259540A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912654A Withdrawn EP1254172A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01918156A Withdrawn EP1254151A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines, et anticorps
EP01914330A Withdrawn EP1252297A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01924084A Withdrawn EP1265910A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01924086A Withdrawn EP1259531A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01910332A Withdrawn EP1255864A1 (fr) 2000-01-31 2001-01-17 Acides nucl iques, proteines et anticorps
EP01920102A Withdrawn EP1254152A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines, et anticorps
EP01908611A Withdrawn EP1261633A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01912652A Withdrawn EP1254171A1 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines et anticorps
EP01910330A Withdrawn EP1255768A2 (fr) 2000-01-31 2001-01-17 Acides nucleiques, proteines, et anticorps

Country Status (1)

Country Link
EP (38) EP1254219A2 (fr)

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9433675B2 (en) 2012-05-23 2016-09-06 Ganymed Pharmaceuticals Ag Combination therapy involving antibodies against claudin 18.2 for treatment of cancer
US9770487B2 (en) 2013-02-20 2017-09-26 Ganymed Pharmaceuticals Ag Combination therapy involving antibodies against claudin 18.2 for treatment of pancreatic adenocarcinoma
US10093736B2 (en) 2012-11-13 2018-10-09 Biontech Ag Agents for treatment of claudin expressing cancer diseases
US10137195B2 (en) 2013-03-18 2018-11-27 Ganymed Pharmaceuticals Gmbh Therapy involving antibodies against Claudin 18.2 for treatment of cancer

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
See references of WO0155314A2 *

Cited By (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9433675B2 (en) 2012-05-23 2016-09-06 Ganymed Pharmaceuticals Ag Combination therapy involving antibodies against claudin 18.2 for treatment of cancer
US10022444B2 (en) 2012-05-23 2018-07-17 Ganymed Pharmaceuticals Ag Combination therapy involving antibodies against Claudin 18.2 for treatment of cancer
US10813996B2 (en) 2012-05-23 2020-10-27 Astellas Pharma Inc. Combination therapy involving antibodies against Claudin 18.2 for treatment of cancer
US12059464B2 (en) 2012-05-23 2024-08-13 Astellas Pharma Inc. Combination therapy involving antibodies against Claudin 18.2 for treatment of cancer
US10093736B2 (en) 2012-11-13 2018-10-09 Biontech Ag Agents for treatment of claudin expressing cancer diseases
US9770487B2 (en) 2013-02-20 2017-09-26 Ganymed Pharmaceuticals Ag Combination therapy involving antibodies against claudin 18.2 for treatment of pancreatic adenocarcinoma
US10314890B2 (en) 2013-02-20 2019-06-11 Astellas Pharma Inc. Combination therapy involving antibodies against claudin 18.2 for treatment of pancreatic cancer
US10946069B2 (en) 2013-02-20 2021-03-16 Astellas Pharma Inc. Combination therapy involving antibodies against claudin 18.2 for treatment of pancreatic cancer
US11826402B2 (en) 2013-02-20 2023-11-28 Astellas Pharma Inc. Combination therapy involving antibodies against claudin 18.2 for treatment of metastatic pancreatic adenocarcinoma
US10137195B2 (en) 2013-03-18 2018-11-27 Ganymed Pharmaceuticals Gmbh Therapy involving antibodies against Claudin 18.2 for treatment of cancer
US11395852B2 (en) 2013-03-18 2022-07-26 Astellas Pharma Inc. Therapy involving antibodies against Claudin 18.2 for treatment of cancer

Also Published As

Publication number Publication date
EP1261618A2 (fr) 2002-12-04
EP1265910A2 (fr) 2002-12-18
EP1252289A2 (fr) 2002-10-30
EP1255776A1 (fr) 2002-11-13
EP1254173A1 (fr) 2002-11-06
EP1254219A2 (fr) 2002-11-06
EP1261703A1 (fr) 2002-12-04
EP1252297A1 (fr) 2002-10-30
EP1254152A2 (fr) 2002-11-06
EP1252176A2 (fr) 2002-10-30
EP1254153A2 (fr) 2002-11-06
EP1261634A1 (fr) 2002-12-04
EP1252290A1 (fr) 2002-10-30
EP1259531A2 (fr) 2002-11-27
EP1254151A1 (fr) 2002-11-06
EP1254172A1 (fr) 2002-11-06
EP1261637A1 (fr) 2002-12-04
EP1255817A1 (fr) 2002-11-13
EP1259526A2 (fr) 2002-11-27
EP1261380A1 (fr) 2002-12-04
EP1255768A2 (fr) 2002-11-13
EP1259642A1 (fr) 2002-11-27
EP1254171A1 (fr) 2002-11-06
EP1259540A1 (fr) 2002-11-27
EP1254147A2 (fr) 2002-11-06
EP1255864A1 (fr) 2002-11-13
EP1254218A2 (fr) 2002-11-06
EP1261633A2 (fr) 2002-12-04
EP1254248A2 (fr) 2002-11-06
EP1261745A2 (fr) 2002-12-04
EP1255778A2 (fr) 2002-11-13
EP1252302A2 (fr) 2002-10-30
EP1252185A1 (fr) 2002-10-30
EP1252303A2 (fr) 2002-10-30
EP1255767A2 (fr) 2002-11-13
EP1263944A2 (fr) 2002-12-11
EP1255777A1 (fr) 2002-11-13

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