WO2011008970A1

WO2011008970A1 - Methods for diagnosing chronic diarrhea through protein secretion analysis

Info

Publication number: WO2011008970A1
Application number: PCT/US2010/042157
Authority: WO
Inventors: Thomas M. Donndelinger
Original assignee: Donndelinger Thomas M
Priority date: 2009-07-16
Filing date: 2010-07-15
Publication date: 2011-01-20

Abstract

Methods for diagnosing chronic diarrhea and other gastrointestinal conditions. In the methods, a sample of gastrointestinal secretions is obtained from a control group; or a group who has been diagnosed with either healthy gastrointestinal tracts or with a gastrointestinal condition, like chronic diarrhea. The control group samples are analyzed in any suitable manner to determine the levels of gastrointestinal secretions, including one or more cytokeratin I subtypes, cytokeratin II subtypes, antimicrobial proteins, mitochondria, and digestive enzymes. The results of the sample analysis is used to create a database containing profiles of normal and abnormal gastrointestinal secretions. As the database is created and specific secretion level abnormalities are identified, patients may be diagnosed with these abnormalities and be treated by adjusting the levels of specific secretions. Gastrointestinal samples from subsequent patients may be analyzed and compared with the database to determine which of the patients' secretion levels, if any, are abnormal.

Description

METHODS FOR DIAGNOSING CHRONIC DIARRHEA THROUGH PROTEIN SECRETION ANALYSIS

CROSS-REFERENCE TO RELATED APPLICATION

[0001] This is a continuation-in-part application of U.S. Patent Application No. 11/876,590, filed October 22, 2007, which is a continuation-in-part application of U.S. Utility Patent Application 11/613,717, filed December 20, 2006, which claims priority to U.S. Provisional Patent Application 60/752,618, filed December 21, 2005, the entire disclosures of which are hereby incorporated by reference.

BACKGROUND

1. The Field of the Invention

[0002] The present disclosure relates to the field of medical diagnosis. More particularly, the present disclosure discusses improved methods for diagnosing or obtaining information about chronic diarrhea and other gastrointestinal disorders in humans or other warm-blooded animals.

2. The Prior State of the Art

[0003] Many people suffer from the medical condition of chronic diarrhea, or diarrhea that lasts for more than two weeks. Although persistent, this problem is usually painless and is generally not accompanied by more serious conditions, such as bleeding, anemia, weight loss, or fatigue. Nevertheless, this condition can be a nuisance and an embarrassment to many people. Accordingly, doctors and researchers have long searched for causes of the ailment as well as its treatments.

[0004] There are many different causes of chronic diarrhea. For example, some types of chronic diarrhea may be caused by infection, which, in turn, may have been caused by parasites, bacteria, viruses, or the like. In other cases, chronic diarrhea may be caused by medications, antibiotics, food additives, or drugs ingested into the body. In yet other cases, chronic diarrhea may be caused by more serious medical conditions, such as cancer, pre- malignant and malignant lesions, tumors, diabetes, thyroid and other endocrine diseases, food allergies, reduced blood flow to the intestine, colitis, and/or Crohn's disease. Previous surgery or radiation treatments on the abdomen or gastrointestinal tract may also be the source of some forms of chronic diarrhea. [0005] Yet, despite the knowledge regarding chronic diarrhea, there are some cases of chronic diarrhea for which there are no known causes. In fact, it is estimated that 20% to 30% of all cases of chronic diarrhea have no known cause. Despite numerous tests and analyses, doctors often cannot pinpoint why some patients suffer from chronic diarrhea.

[0006] In some cases, doctors may advise patients that the chronic diarrhea problem is caused by stress, emotional problems, psychological problems, and so forth. Accordingly, these doctors may suggest that patients change their lifestyle— by reducing stress, seeking professional counseling, etc.— as a means of coping with the chronic diarrhea. Of course, such treatments can be difficult to implement, expensive, drastic, and ineffective. Thus, such treatments are often disfavored.

[0007] Moreover, many of the tests currently used to diagnose chronic diarrhea may require multiple analyses by a doctor. Not only can such a battery of tests require a patient to repeatedly visit the doctor, but more importantly, some of the tests required to diagnose chronic diarrhea may be unreliable as well as uncomfortable, embarrassing, and unpleasant.

[0008] Accordingly, it would be an advancement in the art to provide a new method, which may be easily administered and reliable. Moreover, this new method may also provide doctors and researchers with additional information regarding the cause of the chronic diarrhea. Such a method for diagnosing chronic diarrhea is disclosed herein.

BRIEF SUMMARY

[0009] The present invention is directed to methods for diagnosing or obtaining information about chronic diarrhea in humans or any other desired warm-blooded animals. The invention is based upon a non-binding theory that through one or more apocrine mechanisms, a healthy gastrointestinal tract secretes a variety of diverse proteinaceous substances into the intestines, and more specifically, into the colon. Some non-limiting examples of such proteinaceous excretions include cytokeratin I proteins, cytokeratin II proteins, antimicrobial proteins, mitochondria-containing cell fragments, cytoplasm, mucous, and/or digestive enzymes.

[0010] With respect to cytokeratin I and cytokeratin II secretions, it is theorized that various cytokeratin I and cytokeratin II subtype proteins or subtypes, such as CKl, CK2, CK5, CK6, CK9, CKlO, CK14, and CK16, that are secreted into the gastrointestinal tract may act to stabilize mucous and improve the mucous' ability to attach to cells lining the tract. Accordingly, in this theory, it is believed that the presence of proper levels of certain cytokeratin I and cytokeratin II subtype secretions helps to maintain a healthy protective layer of mucous, which, in turn, controls bacterial antigen access to the cell lining of the gastrointestinal tract.

[0011] Regarding the role of anti-microbial proteins in the gastrointestinal tract, it is theorized that proteins, such as lysozyme, calprotectin, and other polycationic antimicrobials, like histones, may work together or independently to help regulate intestinal flora. For instance, it is believed that lysozyme, calprotectin, and/or histones may have antibacterial characteristics that help purge the intestines of unhealthy microorganisms.

[0012] Similarly, it is theorized that the presence of digestive enzymes may indicate a colonic extension or supplementation to normal digestion. Additionally, under another theory, it is believed that mitochondria secreted in the gastrointestinal tract may react with oxygen and, thereby, make the gastrointestinal tract an anaerobic environment.

[0013] Under the non-binding theories proposed herein, chronic diarrhea and other gastrointestinal disorders, including cancer or disease in the gastrointestinal tract, may be diagnosed by detecting deficient or otherwise abnormal levels of one or more of the aforementioned secretions in the gastrointestinal tract.

[0014] Accordingly, the described methods may include obtaining a sample of gastrointestinal secretion from a patient. The sample may then be analyzed using one or more conventional or novel techniques. The results of the analysis may then be compared with results obtained from the analysis of control samples, or from samples obtained from individuals who have been diagnosed as having healthy intestines, chronic diarrhea, and/or any other condition or disorder of the gastrointestinal tract. Thus, the control samples may comprise normal and abnormal profiles. Also, if appropriate, the abnormal control samples may be further subset into subcategories of chronic diarrhea or other gastrointestinal disorders.

[0015] After the patient's results have been compared with the results of the control samples, any abnormal secretion levels in the patient may be determined. One or more abnormal secretion levels may then be correlated with chronic diarrhea or some other form of gastrointestinal disorder. After diagnosis, the patient may be treated for the disorder through regulation or adjustment of the abnormal secretion level. One non-limiting example of such a treatment includes supplementing a patient with preparations that will release the deficient protein into the patient's colon. Additionally, the results of the sample obtained from the patient may also be used to provide more diagnostic information about the type or cause of the condition. BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

[0016] Figure 1 is a photograph showing the presence of lysozyme in human colonic lumen, wherein the presence of lysozyme is verified through the use of a lysozyme- specific antibody and an immunoperoxidase stain;

[0017] Figure 2 is a photograph showing the presence of lysozyme in human colonic lumen, wherein the presence of lysozyme is verified through the use of a lysozyme- specific antibody and an immunofluorescent stain;

[0018] Figure 3 is a photograph showing the presence of mitochondria in human colonic lumen, wherein the presence of mitochondria is verified through the use of a mitochondria- specific antibody and a fluorescent stain;

[0019] Figure 4 is a photograph showing the presence of amylase in human colonic lumen, wherein the presence of amylase is verified through the use of an amylase- specific antibody and an immunoperoxidase stain; and

[0020] Figure 5 is a photograph showing the presence of amylase in human colonic lumen, wherein the presence of amylase is verified through the use of an amylase- specific antibody and an immunofluorescent stain.

[0021] Together with the following description, the Figures may help demonstrate and explain the principles of the described methods.

DETAILED DESCRIPTION

[0022] The following description supplies specific details in order to provide a thorough understanding. Nevertheless, the skilled artisan would understand that the described methods and any associated techniques can be implemented and used without employing these specific details. Indeed, the described methods can be placed into practice with any modification and can be used in conjunction with any suitable apparatus, systems, components, and/or techniques conventionally used in the industry. For example, while the description below focuses on diagnosing chronic diarrhea in humans, it may also be implemented for any other warm-blooded animal or may be used to diagnose many other gastrointestinal disorders.

[0023] Applicant has discovered that humans and other life forms secrete cytokeratin I subtypes, cytokeratin II subtypes, antimicrobial proteins, mitochondria, and/or digestive enzymes into the gastrointestinal tract. Such secretions may occur in various places throughout the digestive tract and, in particular, may be found in the colon. For example, evidence that antimicrobial proteins, which may include lysozyme, are secreted into the gastrointestinal tract is shown in Figures 1 through 2. Figures 1 through 2 contain light microscopy pictures taken at 1,60OX of samples that were prepared using the methods disclosed in U.S. Patent Application Publication No. 2006-0228772-A1, entitled "Compositions and Methods for Preparing Specimens for Microscopic Analysis," the entire disclosure of which is hereby incorporated by reference.

[0024] Specifically, Figures 1 and 2 are photographs that include arrows indicating the presence of lysozyme in human colonic lumen. While the samples in both Figure 1 and 2 have been treated with a rabbit IgG lysozyme primary antibody, the sample in Figure 1 was treated with an immunoperoxidase secondary antibody while the sample in Figure 2 was treated with an immunofluorescent secondary antibody.

[0025] Similarly, evidence that mitochondrial and digestive enzyme secretions occur in the gastrointestinal tract may be found in Figures 3, 4, and 5, which are also pictures taken using light microscopy according to the aforementioned methods. In particular, through the use of a primary antibody targeted to the ox-phos complex 4 of the mitochondrial subunit 1 and a fluorescent secondary antibody, Figure 3 shows the presence of mitochondria in both the cytoplasm of mucosal cells as well as in the lumen, as is indicated by the arrows. Moreover, Figures 4 and 5 show photographs of human colonic lumen that have been treated with a mouse immunoglobulin (IgG) amylase primary antibody, wherein the presence of amylase is indicated with arrows. While the sample in Figure 4 has been treated with an immunoperoxidase secondary antibody, the sample in Figure 5 has been treated with an immunofluorescent secondary antibody.

[0026] The theory that cytokeratin I subtypes, cytokeratin II subtypes, antimicrobial proteins, mucus, mitochondrial proteins, and/or digestive enzymes are secreted and play a prophylactic role in the gastrointestinal tract provides a basis for the described methods. Although the present methods may involve a variety of steps or processes in any suitable order, a non- limiting example of a typical method is described herein for purpose of illustration. Generally, the described method may comprise collecting samples of gastrointestinal secretions from a control group; or an initial group, or groups, of patients (or humans) who have been diagnosed with healthy gastrointestinal tracts, chronic diarrhea, and/or any other desired form of gastrointestinal disorder. The samples from the control group may be analyzed in order to determine specific secretion levels and may be used to create a database containing profiles of normal and abnormal gastrointestinal secretions as well as any subset thereof. After such a database is created and specific secretion level abnormalities are identified, patients with these abnormalities may be treated by regulating or adjusting the specific secretion levels. Furthermore, gastrointestinal samples from subsequent patients may be analyzed and compared with the database in order to determine which of the patients' secretion levels, if any, are abnormal. Once a specific secretion level abnormality has been identified in a patient, the patient may be treated. In order to provide a better understanding of the aforementioned method, this method is discussed below in more detail.

[0027] As mentioned, the described method may include collecting samples of gastrointestinal secretions from at least one control group and/or from subsequent patients. The control group in the described methods may be made up of any number of patients with any desired characteristic. For instance, the number of patients in a control group may range anywhere from one single patient to groups of millions of patients, or any number in between. Also, patients in the control group may be of any desired age, sex, weight, height, race, ethnicity, socioeconomic class, profession, and the like. Moreover, the patients in the control group may have any known or unknown physical, mental, and/or emotional condition or disorder. For example, patients of the control group may have been previously diagnosed, by any suitable method, as having healthy bowels, chronic diarrhea, and/or another gastrointestinal condition. Some additional non-limiting examples of gastrointestinal conditions may include Crohn's disease, ulcerative colitis, ulcers, cancer, pre-malignant lesions, malignant lesions, etc. Patients in the control group who have been diagnosed with a gastrointestinal disorder may also be subset in any desired manner. For example, patients with chronic diarrhea may be subset into categories or subcategories according to the cause of the diarrhea (e.g., diarrhea caused by disease, parasites, bacteria, viruses, stress, drugs, cancer, abnormal secretion levels, unknown factors, etc.).

[0028] In some embodiments, a sample may be collected from a patient's colon (i.e., ascending colon, transverse colon, descending colon, and/or sigmoid colon). In other embodiments, a sample of gastrointestinal secretions may be collected from another portion of a patient's gastrointestinal tract, which may range from a patient's mouth to a patient's anus. For example, samples may be collected from a patient's small intestine or stomach.

[0029] The collected samples may contain any secretion that can be found in the gastrointestinal tract. For instance, the gastrointestinal samples may contain one or more cytokeratin I subtypes, cytokeratin II subtypes, antimicrobial proteins, cytoplasm, mucous, digestive enzymes, mitochondria, and/or markers for cancer. As used herein, the terms secretion, cytokeratin I subtypes, cytokeratin II subtypes, antimicrobial proteins, mitochondria, digestive enzymes, markers for cancer, and subclasses thereof (e.g., specific proteins) may include gene-spliced variants, post-translational modifications, degradation products, truncations, precursors (e.g., RNA), or other detectable chemical structures that can be used to determine levels of the proteinaceous secretions.

[0030] With respect to cytokeratin I and cytokeratin II subtypes, the gastrointestinal samples may contain the low molecular weight, acidic type I cytokeratins and/or the high molecular weight, basic or neutral type II cytokeratins. Further, the gastrointestinal samples may contain any known or novel form of a cytokeratin II subtype, such as CKl, CK2, CK3, CK4, CK5, CK6, CK7, and CK8, and/or any known or novel form of a cytokeratin I subtype, such as CK9, CKlO, CK12, CK13, CK14, CK16, CK17, CK18, CK19, and CK20. For instance, as will be discussed below in the Examples section, secretions of CKl, CK2, CK5, CK6, CK9, CKlO, CK14, and CK16 have been found in gastrointestinal samples taken from human colons.

[0031] With respect to the digestive enzymes that may be found in the gastrointestinal samples, the samples may include any digestive enzymes found in the gastrointestinal tracts of warm-blooded animals. Some non-limiting examples of such digestive enzymes may include any appropriate form of amylase (e.g., α-amylase, β-amylase, and/or γ-amylase), lipase, peptidase, sucrase, maltase, lactase, isomaltase, eripsin, gelatinase, trypsin, chymotrypsin, etc., and/or combinations thereof.

[0032] Samples of gastrointestinal secretions may be collected in any suitable manner. Accordingly, the samples may be collected from stool samples or while the patient is undergoing endoscopy or surgery. For example, samples of gastrointestinal secretions that contain one or more cytokeratin I subtypes, cytokeratin II subtypes, antimicrobial proteins, and/or another proteinaceous secretions may be collected from stool samples or directly from the colon. Indeed, samples of gastrointestinal secretions containing any gastrointestinal secretion may often be obtained as the patient undergoes endoscopy. Because endoscopy is currently one of the more commonly used tests performed on patients with chronic diarrhea, patients may not need to be subjected to additional procedures in order to accomplish the present methods. Furthermore, endoscopy is usually performed on a patient after the patient's bowel and gastrointestinal system have been purged. Accordingly, if gastrointestinal secretions are collected from a patient during endoscopy, these secretions may likely be substantially clean and free of excrement or other impurities. Thus, gastrointestinal secretions collected in this manner may need little purification in order to be used in the present method.

[0033] Once a sample of gastrointestinal secretions has been collected, the sample may be analyzed using any known or novel technique in order to determine the presence of one or more forms of specific secretions and/or the levels of the specific secretions present in the sample. For instance, some non-limiting examples of methods by which a sample of gastrointestinal secretions may be analyzed may include spectroscopy, chromatography, immunohistochemistry, immunofluorescence, immunoblotting (e.g., Western blotting), enzyme-linked immunosorbant assays (ELISA), various forms of polymerase chain reaction (e.g., PCR, RT-PCR, etc.), or any other appropriate form of biochemical analysis. Indeed, persons skilled in the art may appreciate that other known and novel analytical methods may be used to analyze the gastrointestinal secretions.

[0034] In one example of a method for analyzing samples of gastrointestinal secretions, the samples are analyzed using spectroscopy and/or chromatography. In some embodiments, a sample may be analyzed using mass spectroscopy (MS) or gas chromatography-mass spectroscopy (GC-MS). In other embodiments, gas chromatography-mass spectroscopy mass spectroscopy (GC-MS/MS) may be used in tandem. In yet other embodiments, surface- enhanced laser desorption ionization time-of-flight ("SELDI-TOF") mass spectroscopy, or matrix-assisted laser desorption ionization time-of-flight ("MALDI-TOF") mass spectroscopy may be used to determine the presence and/or levels of particular secretions in a sample.

[0035] Where mass spectroscopic analysis is performed, the samples of gastrointestinal secretions may be prepared for analysis through any commonly known method. For instance, some potential methods of sample preparation may be described in an article by David K. Crockett et al., entitled "Identification of Proteins from Formalin-Fixed Paraffin-Embedded Cells by LC-MS/MS," the entire disclosure of which is herein incorporated by reference. While the Crockett article relates to recovering tissue specimens from paraffin blocks, it is within the level of skill in the art to prepare samples of gastrointestinal secretions for use with mass spectroscopy, GC-MS/MS, and other analytical methods, through many other methods. For instance, before spectroscopic analysis, a sample of gastrointestinal secretions may be separated into its various components by ultracentrifugation.

[0036] As is known in the art, conducting a mass spectrographic analysis on a sample may produce results in the form of a mass chromatogram proteomic pattern with peaks that correspond to the various compounds, proteins, bio-molecules, etc. that are found in the sample. More specifically, the peaks may include information about the proteome of the sample of gastrointestinal secretions, including information about cytokeratin I subtypes; cytokeratin II subtypes; antimicrobial proteins, such as lysozyme or histones; mitochondria; digestive enzymes, such as amylase, lipase, peptidase, etc.; cytoplasm; cell membranes; mucous; cancer markers; and/or other structures or compounds found in the secretions. Thus, the mass spectroscopy results of the gastrointestinal secretions may include a spectrum or "fingerprint" of expressed genetic information relating to the gastrointestinal tract. Additionally, if the components of the secretions were separated first (e.g., through centrifugation), then separate mass spectroscopy analysis may occur, which may provide a specific proteomic pattern for each component.

[0037] In a second example of methods for analyzing samples of gastrointestinal secretions, the sample may be analyzed through any suitable form of immunohistochemistry. For example, monoclonal and/or polyclonal antibodies targeted to one or more specific secretions may be applied to the sample and be allowed to complex with corresponding antigens. In this example, a labeled primary antibody could be applied to an antigen (such as a cytokeratin I subtype, a cytokeratin II subtype, lysozyme, a histone, amylase, lipase, a cancer marker, etc.) in a single stage and a labeled secondary antibody may be used to target a species- specific part of the structure of a primary antibody. In some instances, the use of a secondary antibody may be advantageous because multiple secondary antibodies may bind to a primary antibody and thereby amplify the signal.

[0038] Although any suitable primary and/or secondary antibody(s) may be used to target a desired secretion, some examples of suitable primary antibodies may include anti-cytokeratin (e.g., anti-CKl, anti-CK2, anti-CK3, anti-CK4, anti-CK5, anti-CK6, anti-CK7, anti-CK8, anti-CK9, anti-CK10, anti-CK12, anti-CK13, anti-CK14, anti-CK16, anti-CK17, anti-CK18, anti-CK19, anti-CK20, CK3-11D5, CK3-3E4, etc.), anti-histone H2A, anti-histone H2B, anti- histone H3, anti-histone H4, anti-histone Hl, anti-lysozyme, anti-amylase, anti-lipase, anti- peptidase, anti-cytochrome oxidase, anti- superoxide dismutase, etc. Moreover, antibodies for any or all mitochondrial proteins may be used as primary antibodies. Some non-limiting examples of antibodies to mitochondrial proteins may include anti-cytochrome C, anti- VDAC/Porin, monoclonal anti-mitochondrial pi 10, monoclonal anti-TOM22, etc.

[0039] As previously alluded to, whether antibodies are used alone, in a single stage, or in conjunction with other antibodies, in multiple stages, the primary and/or secondary antibodies may be directly conjugated with a label. A label may be any chemical group or radioactive atom added to a molecule that is used in order to track material through a reaction or to locate material spatially. In some embodiments, a color or radioactivity may be emitted from the site of an antibody-antigen complex and the emissions may be of varying intensities according to the level of antigen present. [0040] Where immunohistochemistry is implemented for gastrointestinal secretion analysis, any suitable label may be used to help identify desired secretions and/or to determine secretion levels present in the samples. Some examples of suitable labels may include biotin, Texas red, fluorescein, rhodamine, green florescent protein, red florescent protein, cyan florescent protein, yellow florescent protein, horseradish peroxidase, alkaline phosphatase, cyanine, ferratin, phycoerythrin, colloidal gold spheres, gold nano-particles, radiolabels (such as P32, S35, C14, H3, and 1125), and the like.

[0041] As is known in the art, the results obtained from immunohistochemistry performed on a sample may allow a person or an instrument to analyze the sample and detect the presence of desired forms of secretions and/or the levels of secretions in the sample. The results from such an analysis may be obtained and interpreted in any suitable manner. For example, where the intensity of staining correlates with the amount of protein of interest, a densitometer or absorptiometer may be used to measure protein concentration in a sample. In a second example, a conventional light microscope using bright-field, phase contrast, Nomarski, and/or dark-field microscopy may be used to identify the presence, and to some extent, the level of one or more secretions according the staining of the labels as well as their intensity. For instance, the number of cells comprising a stained or labeled marker may be estimated through the use of a hemocytometer. In a third example, a microscope with a florescent light (including a confocal microscope) may be used to observe the presence, and to some extent the level, of one or more desired secretions, which can be labeled with a florescent marker, such as fluorescein or rhodamine, via one or more antibodies. In a fourth example, one or more secretions marked with a label, such as ferratin or colloidal gold spheres, may be observed and intensity levels may be noticed through the use of an electron microscope (e.g., transmission, scanning, and/or cryoelectron). In yet a fifth example, one or more secretions marked with a radioactive label may be observed and, to some extent, quantified in a sample through the use of a Geiger counter or film that is sensitive to radioactivity.

[0042] In a third example of methods for analyzing samples of gastrointestinal secretions, any suitable form of immunoblotting may be used to determine the presence of specific secretions (including detectable forms thereof) as well as the levels of one or more specific secretions in the sample. For instance, secretions from a sample may be denatured and then be separated through sodium dodecyl sulfate poly-acrylamide gel electrophoresis (SDS/PAGE). After the proteins have been separated, they may be moved from within the gel onto a membrane in order to make the proteins accessible to antibody detection. Such a membrane may be made of nitrocellulose, polyvinylidene difluoride (PVDF), or another appropriate material. After being transferred to the membrane, desired proteins may be probed (detected) using antibodies specific to the target protein, as explained above. For instance, a labeled anti-cytokeratin antibody targeted to a specific subtype of cytokeratin (e.g., CKl, CK2, CK5, CK6, CK9, CKlO, CK14, or CK 16) may be complexed with the corresponding cytokeratin subtype that is found in the gastrointestinal secretion.

[0043] After the primary or secondary antibody produces a signal and any unbound proteins have been washed away, results from sample analysis may be obtained. For instance, size approximations may be taken by comparing stained bands of labeled protein to a standardized marker or ladder loaded during electrophoresis and the amount of target protein may also be indexed to a control. In this manner, the presence of a specific secretion, as well as its level in the sample, may be obtained.

[0044] No matter the method of sample analysis, the results of various analyzed samples may be compared to each other and may be used to create a database. Such a database may be created in any desired manner. For example, the results from samples of gastrointestinal secretions of patients diagnosed with various forms of chronic diarrhea or other bowel disorders may be grouped and compared with the results of samples obtained from patients who have been diagnosed as having healthy bowels. By way of non-limiting illustration, the proteomic patterns obtained through spectroscopy of the samples obtained from the various groups (e.g., patients with healthy bowels and patients with chronic diarrhea) may be compared and any differences between the group's proteomes may be determined. Similarly, immunohistochemical results, PCR results, chromatography results, and/or results from other biochemical analysis from samples obtained from the various groups may be compared and the different results (e.g., stain presence, staining intensity, protein presence, protein concentration, etc.) may be determined.

[0045] By comparing the results from samples obtained from patients with healthy bowels against the results from samples obtained from patients with various gastrointestinal conditions (e.g., chronic diarrhea, cancer, ulcers, etc.), researchers, doctors, technicians, etc. may be able to identify the secretions present in healthy or normal bowels as well as the normal levels of the various secretions. Such a comparison may also allow researchers, doctors, technicians, etc. to identify the absence or presence of certain secretions as well as levels of particular secretions that are associated with various gastrointestinal conditions.

[0046] Such a database may be used for any purpose that aids in the diagnosis or study of chronic diarrhea or another gastrointestinal disorder. In one example of the utility of such a database, researchers may observe that healthy colons contain specific subtypes of cytokeratin I (e.g., CK16) and/or cytokeratin II (e.g., CK5) and may further identify normal ranges for levels of the cytokeratin I and/or the cytokeratin II subtypes in healthy colons. Furthermore, researchers may observe that patients who have been diagnosed with chronic diarrhea lack one or more specific subtypes of cytokeratin I and/or cytokeratin II in the colon, or at least have abnormal levels of one or more cytokeratin I and/or cytokeratin II subtypes (e.g., levels of the specific cytokeratin I and/or cytokeratin II subtypes may be above or below the range of the levels of the corresponding cytokeratin I and/or cytokeratin II subtypes found in healthy colons).

[0047] In another similar example, the comparison of the results of samples of gastrointestinal secretions from patients with healthy colons to the results of patients diagnosed with chronic diarrhea may reveal that patients who suffer from chronic diarrhea have one or more combinations of abnormal levels of mitochondria, antimicrobial proteins (e.g., lysozyme, histones, calprotectin, and/or other polycationic antimicrobials), and/or digestive enzymes (e.g., amylase, lipase, etc), where abnormal refers to levels that are above or below those found in healthy patients. By way of non-limiting illustration, the comparison of antimicrobial protein levels from patients diagnosed with healthy bowels and patients diagnosed with chronic diarrhea may reveal that a concentration of an antimicrobial protein (e.g., a subtype of cytokeratin I and/or II) that is 5%, 10%, 20%, or any other determined percent above or below the normal levels found in patients with healthy bowels is indicative of chronic diarrhea.

[0048] In still another non-limiting example of the utility of such a database, a comparison between the secretions from healthy gastrointestinal tracts and gastrointestinal tracts that have been diagnosed with cancer may reveal the presence of known cancer markers, which may indicate a propensity for or the presence of cancer. Moreover, such a comparison may also be used to identify additional cancer markers that have heretofore been unidentified. In sum, the characteristics of bowels with various gastrointestinal disorders may be identified and one or more abnormal profiles may be created.

[0049] After a database has been created, samples from subsequent patients may be compared with the database and be used to diagnose gastrointestinal conditions in the subsequent patients. For example, by comparing the proteomic pattern, immunohistochemical staining pattern, or other secretion analysis results from a patient's sample to the database, an instrument or individual may be able to identify any abnormalities in the patient's gastrointestinal secretion levels. Also, according to the type of abnormality, the instrument or individual may be able to identify the type or types of gastrointestinal condition the patient has. For instance, an individual may be able to diagnose a patient as having a form of chronic diarrhea associated with a deficiency of a cytokeratin I subtype and/or cytokeratin II subtype (e.g., CK9) in the colon. Thus, by obtaining and analyzing mass spectroscopic proteomic pattern results, or any other form of results, from a particular patient and then comparing the results with those of known profiles in a database, an instrument or individual may be able to diagnose chronic diarrhea and/or another disorder.

[0050] Although the comparison of samples may be done in any appropriate manner, adaptive artificial intelligence bioinformatics may be used to read the pathologic states reflected in the proteomic patterns obtained through mass spectroscopy. Bioinformatic pattern recognition tools can recognize complex data from thousands of proteins simultaneously. This information may indicate that the patient has chronic diarrhea or any other gastrointestinal disorder and provide diagnostic information about the type or cause of the condition. Such a method may both speed comparisons as well as increase their accuracy.

[0051] As more results are obtained and analyzed, the database may be further subset in any desired manner. Thus, as the database and comparisons reveal more information about gastrointestinal secretions and their roles, the database may also reflect the advanced knowledge and thereby make it easier to diagnose previously un-diagnosable forms of chronic diarrhea and/or other gastrointestinal conditions.

[0052] For example, a database may begin simply with a healthy or normal profile and an abnormal or chronic diarrhea profile. As more samples are collected and differences between the samples are identified, each of the categories may be further subset. For instance, the chronic diarrhea category may be split into several subcategories, such as chronic diarrhea caused by a cytokeratin deficiency, chronic diarrhea caused by antimicrobial protein deficiencies, chronic diarrhea caused by digestive enzyme deficiencies, chronic diarrhea caused by histone deficiencies, chronic diarrhea caused by mitochondria deficiencies, chronic diarrhea caused by cancer, etc. In this example, each of the subcategories could be further subset. For instance, the category of chronic diarrhea caused by a cytokeratin deficiency may be subset into different categories of specific cytokeratin deficiencies. By way of non- limiting example, the category of chronic diarrhea caused by a cytokeratin deficiency can be subset into two subclasses, namely chronic diarrhea caused by a deficiency of a cytokeratin I subtype and chronic diarrhea caused by a deficiency of cytokeratin II subtype. In this example, the two subclasses can be further subset into chronic diarrhea caused by deficiencies in specific subtypes of cytokeratin I and II (e.g., CK 1, CK 2, CK 14, etc.). Additionally, in this example, the subclasses could be further subdivided. For instance, the subclasses could be further divided to include abnormal levels of a combination of secretions (e.g., a subclass for abnormal levels of CK 14, amylase, and histones). This process of subsetting may be repeated many subsequent times, according to any desired criteria.

[0053] Moreover, as differences are identified between the gastrointestinal secretions of healthy gastrointestinal tracts and the secretions of gastrointestinal tracts with a disorder, like chronic diarrhea, any effective treatments for such conditions may be developed. For example, after ranges of specific secretion levels in healthy colons have been identified, the levels of the specific secretion levels in patients with unhealthy colons may be regulated or adjusted in any suitable manner so as to control, reduce, and/or eliminate the condition. For instance, a patient who is identified as having a form of chronic diarrhea that is associated with a deficiency of one or more cytokeratin I and/or cytokeratin II subtypes in the colon may use dietary supplements, injections, transdermal patches, delayed release supplements, or suppositories that release a suitable form of the deficient cytokeratin I and/or cytokeratin II subtype into the colon. In yet another example of a method for treating a patient who has been diagnosed with chronic diarrhea, a patient may be prescribed antimicrobials, reducing agents, polycationic compounds, or other supplements alone or with one or more combined in a cocktail depending on the patient's individual secretion composition.

[0054] The following examples are given to illustrate an embodiment within the scope of the present invention. These are given by way of example only, and it is understood that the following examples are not comprehensive or exhaustive of the many types of embodiments of the present invention in accordance with the present invention.

EXAMPLES

[0055] In one example of forming a database according to one embodiment of the invention, colon samples were taken from two different colons and the protein secretions from the colons were compared through GC-MS. Specifically, lμm sections were taken from the colons and 6 μg samples were removed from the sections through laser dissection. The 6 μg samples were then prepared in the same manner and analyzed with GC-MS. This analysis of the first and second samples revealed the results depicted in Tables 1 and 2.

[0056] Table 1. Experimental Results from the First Colon Sample.

Type of Proteinaceous Secretion Detected Percentage of Total Spectra

CKl 0.95% CK9 0.67%

CK2 0.25%

CKlO 0.33%

CK14 0.15%

CK5 0.05%

CK6A 0.06%

CK16 0.04%

Dermicidin Precursor 0.03%

Serum Albumin Precursor 0.05%

[0057] Table 2. Experimental results from second colon sample.

Type of Proteinaceous Secretion Detected Percentage of Total Spectra

CKl 0.64%

CK9 0.55%

CK2 0.23%

CKlO 0.28%

CK14 0.15%

CK5 0.05%

CK6A 0.06%

CK14 0.05%

Lysozyme Precursor 0.06%

Trypsin Precursor 0.58%

Serum Albumin Precursor 0.06%

Hornerin (Q86YZ3) 0.06%

Filaggrin (P20930) 0.04%

Outer Membrane Protein Precursor - E. coli 0.03%

O157:H7 (P0A911)

[0058] Specifically, Tables 1 and 2 show that the first and second colon samples contained a variety of proteinaceous secretions, including CKl, CK2, CK5, CK6A, CK9, CKlO, CK14, CK16, lysozyme, trypsin, hornerin, serum albumin precursor, filaggrin, and/or the outer membrane protein precursor for e. coli. By correlating any known diagnosis of these colon samples (e.g., whether one colon is healthy and whether one colon suffers from chronic diarrhea) with the obtained GC-MS fingerprints, the described database may be started. This database can then be expanded as additional colon samples having known diagnosis are tested, compared, and the results are entered into the database.

[0059] The present invention may be embodied in other specific forms without departing from its methods or other essential characteristics as broadly described herein and claimed hereinafter. The described embodiments and examples are to be considered in all respects only as illustrative, and not as restrictive or limiting. The scope of the invention is, therefore, indicated by the appended claims, rather than by the foregoing description. All changes that come within the meaning and range of equivalency of the claims are to be embraced within their scope.

Claims

CLAIMS:

1. A method for diagnosing a gastrointestinal disorder in a warm-blooded animal comprising:

obtaining a sample of a gastrointestinal secretion from the warm-blooded animal; analyzing the sample of gastrointestinal secretion to determine whether a level of a cytokeratin in the sample is abnormal; and

correlating an abnormal level of the cytokeratin in the sample with the gastrointestinal disorder in the warm-blooded animal from which the sample was obtained.

2. The method of claim 1, wherein the sample of gastrointestinal secretion is obtained from a colon of the warm-blooded animal.

3. The method of claim 2, wherein the gastrointestinal disorder is chronic diarrhea.

4. The method of claim 1, wherein the cytokeratin is selected from a subtype of cytokeratin I and subtype of cytokeratin II.

5. The method of claim 1, further comprising analyzing the sample of

gastrointestinal secretion to determine whether levels of digestive enzymes, mitochondria, or antimicrobial proteins in the sample are abnormal, and correlating an abnormal level of digestive enzymes, mitochondria, or antimicrobial proteins in the sample with the

gastrointestinal disorder in the warm-blooded animal from which the sample was obtained.

6. The method of claim 5, wherein the digestive enzymes comprise amylase, lipase, and peptidase.

7. The method of claim 5, wherein the antimicrobial proteins are selected from lysozyme, calprotectin, histones, and other polycationic antimicrobials.

8. The method of claim 1, wherein the abnormal level comprises a deficiency.

9. The method of claim 3, wherein the method further comprises treating the warm-blooded animal with chronic diarrhea by adjusting or regulating abnormal level of the cytokeratin in the warm-blooded animal with chronic diarrhea.

10. The method of claim 1, wherein the method further comprise comparing results obtained from an analysis performed on the sample of gastrointestinal secretions obtained from the warm-blooded animal with results obtained from analyses performed on a control group in order to determine the differences between each.

11. The method of claim 10, wherein the control group comprises warm-blooded animals diagnosed as having a healthy colon.

12. The method of claim 11, wherein the control group further comprises warmblooded animals that have been diagnosed with chronic diarrhea or another gastrointestinal disorder.

13. A method for diagnosing chronic diarrhea in a warm-blooded animal comprising:

obtaining a sample of a gastrointestinal secretion from a colon of the warm-blooded animal;

analyzing the sample of gastrointestinal secretion to determine the sample's levels of a cytokeratin selected from a subtype of cytokeratin I and cytokeratin II;

comparing results obtained from the analysis of the sample with results obtained from a control group in order to determine if the levels of the cytokeratin in the sample are abnormal; and

correlating an abnormal level of the cytokeratin in the sample with chronic diarrhea in the warm-blooded animal from which the sample was obtained.

14. The method of claim 13, further comprising analyzing the sample of gastrointestinal secretion to determine whether levels of digestive enzymes, mitochondria, or antimicrobial proteins in the sample are abnormal, and correlating an abnormal level of digestive enzymes, mitochondria, or antimicrobial proteins in the sample with chronic diarrhea in the warm-blooded animal from which the sample was obtained.

15. The method of claim 13, wherein the cytokeratin is selected from CKl, CK2, CK5, CK6, CK9, CKlO, CK14, CK16, and combinations thereof.

16. The method of claim 13, wherein the abnormal level of the cytokeratin comprises a deficiency.

17. The method of claim 13, wherein the method further comprises treating the warm-blooded animal with chronic diarrhea by adjusting or regulating the abnormal level of the cytokeratin.

18. The method of claim 14, wherein the antimicrobial proteins are selected from lysozyme, calprotectin, histones, and other polycationic antimicrobials.

19. The method of claim 13, wherein the control group comprises warm-blooded animals diagnosed as having a healthy colon.

20. The method of claim 19, wherein the control group further comprises warmblooded animals diagnosed as having chronic diarrhea or another gastrointestinal disorder.