Reagents and methods useful for detecting diseases of the gastrointestinal tract

Abstract

A set of contiguous and partially overlapping cDNA sequences and polypeptides encoded thereby, designated as CS193 and transcribed from GI tract tissue, are described. These sequences are useful for the detecting, diagnosing, staging, monitoring, prognosticating, preventing or treating, or determining the predisposition of an individual to diseases and conditions of the GI tract, such as GI tract cancer. Also provided are antibodies which specifically bind to CS193-encoded polypeptide or protein, and agonists or inhibitors which prevent action of the tissue-specific CS193 polypeptide, which molecules are useful for the therapeutic treatment of GI tract diseases, tumors or metastases.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application is a continuation-in-part of U.S. application Ser. No. 08 / 828,856, filed Mar. 31, 1997, from which priority is claimed pursuant to 35 U.S.C. § 120 and which is incorporated herein by reference in its entirety.BACKGROUND OF THE INVENTION [0002] The invention relates generally to detecting diseases of the gastrointestinal tract organs, and more particularly, relates to reagents such as polynucleotide sequences and the polypeptide sequences encoded thereby, as well as methods which utilize these sequences, which are useful for detecting, diagnosing, staging, monitoring, prognosticating, preventing or treating, or determining predisposition to diseases and conditions of the GI tract such as cancer. [0003] The organs of the GI tract include the esophagus, stomach, small and large intestines, rectum and pancreas. Of the approximately 225,900 new cases of GI tract cancer projected for the United States during 1996, 131,200 wil...

AI Technical Summary

Benefits of technology

[0013] The present invention further provides a method of detecting a target CS193 polynucleotide in a test sample suspected of containing target CS193 polynucleotides, which comprises (a) contacting the test sample with at least one CS193 oligonucleotide as a sense primer and at least one CS193 oligonucleotide as an anti-sense primer, and amplifying same to obtain a first stage reaction product; (b) contacting the first stage reaction product with at least one other CS193 oligonucleotide to obtain a second stage reaction product, with the proviso that the other CS193 oligonucleotide is located 3′ to the CS193 oligonucleotides utilized in step (a) and is complementary to the first stage reaction product; and (c) detecting the second stage reaction product as an indication of the presence of a target CS193 polynucleotide in the test sample. The CS193 oligonucleotides selected as reagents in the method have at least 50% identity to a sequence selected from the group consisting of SEQUENCE ID NOS 1-18, and fragments or complements thereof. Amplification may be performed by the polymerase chain reaction. The test sample can be reacted either directly or indirectly with a solid phase prior to performing the method, or prior to amplification, or prior to detection. The detection step also comprises utilizing a detectable label capable of generating a measurable signal; further, the detectable label can be attached to a solid phase. Test kits useful for detecting target CS193 polynucleotides in a test sample are also provided which comprise a container containing at least one CS193-specific polynucleotide selected from the group consisting of SEQUENCE ID NOS 1-18, and fragments or complements thereof. These test kits further comprise containers with tools useful for collecting test samples (such as, for example, blood, urine, saliva and stool). Such tools include lancets and absorbent paper or cloth for collecting and stabilizing blood; swabs for collecting and stabilizing saliva; and cups for collecting and stabilizing urine or stool samples. Collection materials, such as papers, cloths, swabs, cups, and the like, may optionally be treated to avoid denaturation or irreversible adsorption of the sample. The collection materials also may be treated with or contain preservatives, stabilizers or antimicrobial agents to help maintain the integrity of the specimens.

Problems solved by technology

In addition to its high incidence, GI tract cancers can be extremely lethal; for example, greater than 97% of pancreatic cancer patients will die of the disease.

However, only few GI tract cancers are detected at this stage.

Although FOBT is noninvasive, simple and inexpensive, its sensitivity is low; for example, sensitivity for detecting colorectal cancer was only 26% in one study.

Further, although flexible sigmoidoscopy is highly sensitive for detecting early cancer and precursor polyps, it is invasive, costly, and too technically demanding to be used for routine screening.

These procedures are invasive and costly.

Moreover, an erroneous diagnosis can result from any of these procedures due to technical reasons, the subjective interpretation of results, or lack of sensitivity of the procedure.

Inaccurate staging can result in poor therapeutic decisions and is a major clinical problem in colorectal cancer.

These monitoring techniques, however, have failed to provide an accurate and effective means to monitor the progress of these patients.

Currently, no universally acceptable marker(s) exist(s) for the early detection of pancreatic, stomach, and esophageal cancers.

Images