# Patent

## Title
Method of diagnosing, monitoring, and staging colon cancer

## Abstract

The present invention provides a new method for detecting, diagnosing, monitoring, staging, and prognosticating colon cancer.

## Background
This application claims benefit of U.S. Provisional No. 60/086,266 filed May 21, 1998.


FIELD OF THE INVENTION
This invention relates, in part, to newly developed assays for detecting, diagnosing, monitoring, staging, and prognosticating cancers, particularly colon cancer.
BACKGROUND OF THE INVENTION
Colon cancer is the second most frequently diagnosed malignancy in the United States. Cancer of the gastrointestinal tract, especially colon cancer, is a highly treatable and often a curable disease when localized to the bowel. However, currently colon cancer is the second most common cause of cancer death. Surgery is the primary treatment and results in cure in approximately 50% of patients. Recurrence following surgery is a major problem and often is the ultimate cause of death. The prognosis of colon cancer is clearly related to the degree of penetration of the tumor through the bowel wall and the presence or absence of nodal involvement. These two characteristics form the basis for all staging systems developed for this disease. Bowel obstruction and bowel perforation are indicators of poor prognosis. Elevated pretreatment serum levels of carcinoembryonic antigen (CEA) and carbohydrate antigen 19-9 (CA 19-9) also have negative prognostic significance.
Because of the frequency of the disease (approximately 160,000 new cases of colon cancer per year), the identification of high-risk groups, the demonstrated slow growth of primary lesions, the better survival of early-stage lesions, and the relative simplicity and accuracy of screening tests, screening for colon cancer should be a part of routine care for all adults starting at age 50, especially those with first-degree relatives with colorectal cancer.
Procedures used for detecting, diagnosing, monitoring, staging, and prognosticating colon cancer are of critical importance to the outcome of the patient. For example, patients diagnosed with early colon cancer generally have a much greater five-year survival rate as compared to the survival rate for patients diagnosed with distant metastasized colon cancer. Treatment decisions are usually made in reference to the older Dukes or the Modified Astler-Coller (MAC) classification schema for staging. However, new diagnostic methods which are more sensitive and specific for detecting early colon cancer are clearly needed.
Further, colon cancer patients must be closely monitored following initial therapy and during adjuvant therapy to determine response to therapy and to detect persistent or recurrent disease of metastasis. Thus, there is clearly a need for a colon cancer marker which is more sensitive and specific in detecting colon cancer recurrence.
Another important step in managing colon cancer is to determine the stage of the patient's disease. Stage determination has potential prognostic value and provides criteria for designing optimal therapy. Currently, pathological staging of colon cancer is preferable over clinical staging as pathological staging provides a more accurate prognosis. However, clinical staging would be preferred were the method of clinical staging at least as accurate as pathological staging because it does not depend on an invasive procedure to obtain tissue for pathological evaluation. Staging of colon cancer would be improved by detecting new markers in cells, tissues, or bodily fluids which could differentiate between different stages of invasion.
In the present invention, methods are provided for detecting, diagnosing, monitoring, staging, and prognosticating colon cancers, particularly colon, stomach, and small intestine cancer, via nine (9) Colon Specific Genes (CSGs). The nine CSGs refer, among other things, to native proteins expressed by the genes comprising the polynucleotide sequences of any of SEQ ID NO:1, 2, 3, 4, 5, 6, 7, 8 or 9. In the alternative, what is meant by the nine CSGs as used herein, means the native mRNAs encoded by the genes comprising any of the polynucleotide sequences of SEQ ID NO:1, 2, 3, 4, 5, 6, 7, 8 or 9 or levels of the genes comprising any of the polynucleotide sequences of SEQ ID NO:1, 2, 3, 4, 5, 6, 7, 8 or 9.
Other objects, features, advantages and aspects of the present invention will become apparent to those of skill in the art from the following description. It should be understood, however, that the following description and the specific examples, while indicating preferred embodiments of the invention, are given by way of illustration only. Various changes and modifications within the spirit and scope of the disclosed invention will become readily apparent to those skilled in the art from reading the following description and from reading the other parts of the present disclosure.
SUMMARY OF THE INVENTION
Toward these ends, and others, it is an object of the present invention to provide a method for diagnosing the presence of colon cancer in a patient which comprises measuring levels of CSG in a sample of cells, tissue or bodily fluid from the patient and comparing the measured levels of CSG with levels of CSG in preferably the same cells, tissue, or bodily fluid type of a control, wherein an increase in the measured CSG levels in the patient versus levels of CSG in the control is associated with colon cancer.
Another object of the present invention is to provide a method of diagnosing metastatic colon cancer in a patient which comprises measuring CSG levels in a sample of cells, tissue, or bodily fluid from the patient and comparing the measured CSG levels with levels of CSG in preferably the same cells, tissue, or bodily fluid type of a control, wherein an increase in measured CSG levels in the patient versus levels of CSG in the control is associated with a cancer which has metastasized.
Another object of the present invention is to provide a method of staging colon cancer in a patient which comprises identifying a patient having colon cancer, measuring levels of CSG in a sample of cells, tissues, or bodily fluid obtained from the patient, and comparing the measured CSG levels with levels of CSG in preferably the same cells, tissue or bodily fluid type of a control. An increase in measured CSG levels in the patient versus CSG levels in the control can be associated with a cancer which is progressing while a decrease or equivalent level of CSG measured in the patient versus the control can be associated with a cancer which is regressing or in remission.
Another object of the present invention is to provide a method of monitoring colon cancer in a patient for the onset of metastasis. The method comprises identifying a patient having colon cancer that is not known to have metastasized, periodically measuring levels of CSG in a sample of cells, tissues, or bodily fluid obtained from the patient, and comparing the measured CSG levels with levels of CSG in preferably the same cells, tissue, or bodily fluid type of a control, wherein an increase in measured CSG levels versus control CSG levels is associated with a cancer which has metastasized.
Yet another object of the present invention is to provide a method of monitoring the change in stage of colon cancer in a patient which comprises identifying a patient having colon cancer, periodically measuring levels of CSG in a sample of cells, tissue, or bodily fluid obtained from the patient, and comparing the measured CSG levels with levels of CSG in preferably the same cells, tissues, or bodily fluid type of a control wherein an increase in measured CSG levels versus the control CSG levels is associated with a cancer which is progressing and a decrease in the measured CSG levels versus the control CSG levels is associated with a cancer which is regressing or in remission.
Other objects, features, advantages and aspects of the present invention will become apparent to those of skill in the art from the following description. It should be understood, however, that the following description and the specific examples, while indicating preferred embodiments of the invention, are given by way of illustration only. Various changes and modifications within the spirit and scope of the disclosed invention will become readily apparent to those skilled in the art from reading the following description and from reading the other parts of the present disclosure.
DESCRIPTION OF THE INVENTION
The present invention relates to diagnostic assays and methods, both quantitative and qualitative for detecting, diagnosing, monitoring, staging, and prognosticating cancers by comparing levels of CSG with those of CSG in a normal human control. What is meant by “levels of CSG” as used herein, means levels of the native protein expressed by the genes comprising the polynucleotide sequence of any of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8 or 9. In the alternative, what is meant by “levels of CSG” as used herein, means levels of the native mRNA encoded by any of the genes comprising any of the polynucleotide sequences of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8 or 9 or levels of the gene comprising any of the polynucleotide sequence of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8 or 9. Such levels are preferably measured in at least one of, cells, tissues and/or bodily fluids, including determination of normal and abnormal levels. Thus, for instance, a diagnostic assay in accordance with the invention for diagnosing over-expression of any one of the CSG proteins compared to normal control bodily fluids, cells, or tissue samples may be used to diagnose the presence of cancers, including colon cancer. Any of the nine CSGs may be measured alone in the methods of the invention, or all together or any combination of the nine.
By “control” it is meant a human patient without cancer and/or non cancerous samples from the patient, also referred to herein as a normal human control; in the methods for diagnosing or monitoring for metastasis, control may also include samples from a human patient that is determined by reliable methods to have colon cancer which has not metastasized.
All the methods of the present invention may optionally include measuring the levels of other cancer markers as well as CSG. Other cancer markers, in addition to CSG, useful in the present invention will depend on the cancer being tested and are known to those of skill in the art.
Diagnostic Assays
The present invention provides methods for diagnosing the presence of colon cancer by analyzing for changes in levels of CSG in cells, tissues or bodily fluids compared with levels of CSG in cells, tissues or bodily fluids of preferably the same type from a normal human control, wherein an increase in levels of CSG in the patient versus the normal human control is associated with the presence of colon cancer. Without limiting the instant invention, typically, for a quantitative diagnostic assay a positive result indicating the patient being rested has cancer is one in which cells, tissues, or bodily fluid levels of the cancer marker, such as CSG, are at least two times higher, and most preferably are at least five times higher, than in preferably the same cells, tissues, or bodily fluid of a normal human control.
The present invention also provides a method of diagnosing metastatic colon cancer in a patient having colon cancer which has not yet metastasized for the onset of metastasis. In the method of the present invention, a human cancer patient suspected of having colon cancer which may have metastasized (but which was not previously known to have metastasized) is identified. This is accomplished by a variety of means known to those of skill in the art. For example, in the case of colon cancer, patients are typically diagnosed with colon cancer following traditional detection methods.
In the present invention, determining the presence of CSG level in cells, tissues, or bodily fluid, is particularly useful for discriminating between colon cancer which has not metastasized and colon cancer which has metastasized. Existing techniques have difficulty discriminating between colon cancer which has metastasized and colon cancer which has not metastasized and proper treatment selection is often dependent upon such knowledge.
In the present invention, the cancer marker levels measured in such cells, tissues, or bodily fluid is CSG, and are compared with levels of CSG in preferably the same cells, tissue, or bodily fluid type of a normal human control. That is, if the cancer marker being observed is just CSG in serum, this level is preferably compared with the level of CSG in serum of a normal human patient. An increase in the CSG in the patient versus the normal human control is associated with colon cancer which has metastasized.
Without limiting the instant invention, typically, for a quantitative diagnostic assay a positive result indicating the cancer in the patient being tested or monitored has metastasized is one in which cells, tissues, or bodily fluid levels of the cancer marker, such as CSG, are at least two times higher, and most preferable are at least five times higher, than in preferably the same cells, tissues, or bodily fluid of a normal patient.
Normal human control as used herein includes a human patient without cancer and/or non cancerous samples from the patient; in the methods for diagnosing or monitoring for metastasis, normal human control may also include samples from a human patient that is determined by reliable methods to have colon cancer which has not metastasized.
Staging
The invention also provides a method of staging colon cancer in a human patient.
The method comprises identifying a human patient having such cancer; analyzing a sample of cells, tissues, or bodily fluid from such patient for CSG. Then, the method compares CSG levels in such cells, tissues, or bodily fluid with levels of CSG in preferably the same cells, tissues, or bodily fluid type of a normal human control sample, wherein an increase in CSG levels in the patient versus the normal human control is associated with a cancer which is progressing and a decrease in the levels of CSG is associated with a cancer which is regressing or in remission.
Monitoring
Further provided is a method of monitoring colon cancer in a human having such cancer for the onset of metastasis. The method comprises identifying a human patient having such cancer that is not known to have metastasized; periodically analyzing a sample of cells, tissues, or bodily fluid from such patient for CSG; comparing the CSG levels in such cells, tissue, or bodily fluid with levels of CSG in preferably the same cells, tissues, or bodily fluid type of a normal human control sample, wherein an increase in CSG levels in the patient versus the normal human control is associated with a cancer which has metastasized.
Further provided by this inventions is a method of monitoring the change in stage of colon cancer in a human having such cancer. The method comprises identifying a human patient having such cancer; periodically analyzing a sample of cells, tissues, or bodily fluid from such patient for CSG; comparing the CSG levels in such cells, tissue, or bodily fluid with levels of CSG in preferably the same cells, tissues, or bodily fluid type of a normal human control sample, wherein an increase in CSG levels in the patient versus the normal human control is associated with a cancer which is progressing in stage and a decrease in the levels of CSG is associated with a cancer which is regressing in stage or in remission.
Monitoring such patient for onset of metastasis is periodic and preferably done on a quarterly basis. However, this may be more or less frequent depending on the cancer, the particular patient, and the stage of the cancer.
Assay Techniques
Assay techniques that can be used to determine levels of gene expression, such as CSG of the present invention, in a sample derived from a host are well-known to those of skill in the art. Such assay methods include radioimmunoassays, reverse transcriptase PCR (RT-PCR) assays, immunohistochemistry assays, in situ hybridization assays, competitive-binding assays, Western Blot analyses and ELISA assays. Among these, ELISAs are frequently preferred to diagnose a gene's expressed protein in biological fluids. An ELISA assay initially comprises preparing an antibody, if not readily available from a commercial source, specific to CSG, preferably a monoclonal antibody. In addition a reporter antibody generally is prepared which binds specifically to CSG. The reporter antibody is attached to a detectable reagent such as radioactive, fluorescent or enzymatic reagent, for example horseradish peroxidase enzyme or alkaline phosphatase.
To carry out the ELISA, antibody specific to CSG is incubated on a solid support, e.g., a polystyrene dish, that binds the antibody. Any free protein binding sites on the dish are then covered by incubating with a non-specific protein such as bovine serum albumin. Next, the sample to be analyzed is incubated in the dish, during which time CSG binds to the specific antibody attached to the polystyrene dish. Unbound sample is washed out with buffer. A reporter antibody specifically directed to CSG and linked to horseradish peroxidase is placed in the dish resulting in binding of the reporter antibody to any monoclonal antibody bound to CSG. Unattached reporter antibody is then washed out. Reagents for peroxidase activity, including a calorimetric substrate are then added to the dish. Immobilized peroxidase, linked to CSG antibodies, produces a colored reaction product. The amount of color developed in a given time period is proportional to the amount of CSG protein present in the sample. Quantitative results typically are obtained by reference to a standard curve.
A competition assay may be employed wherein antibodies specific to CSG attached to a solid support and labeled CSG and a sample derived from the host are passed over the solid support and the amount of label detected attached to the solid support can be correlated to a quantity of CSG in the sample. Nucleic acid methods may be used to detect CSG mRNA as a marker for colon cancer. Polymerase chain reaction (PCR) and other nucleic acid methods, such as ligase chain reaction (LCR) and nucleic acid sequence based amplification (NASABA), can be used to detect malignant cells for diagnosis and monitoring of various malignancies. For example, reverse-transcriptase PCR (RT-PCR) is a powerful technique which can be used to detect the presence of a specific mRNA population in a complex mixture of thousands of other mRNA species. In RT-PCR, an mRNA species is first reverse transcribed to complementary DNA (cDNA) with use of the enzyme reverse transcriptase; the cDNA is then amplified as in a standard PCR reaction. RT-PCR can thus reveal by amplification the presence of a single species of mRNA. Accordingly, if the mRNA is highly specific for the cell that produces it, RT-PCR can be used to identify the presence of a specific type of cell.
Hybridization to clones or oligonucleotides arrayed on a solid support (i.e., gridding) can be used to both detect the expression of and quantitate the level of expression of that gene. In this approach, a cDNA encoding the CSG gene is fixed to a substrate. The substrate may be of any suitable type including but not limited to glass, nitrocellulose, nylon or plastic. At least a portion of the DNA encoding the CSG gene is attached to the substrate and then incubated with the analyte, which may be RNA or a complementary DNA (cDNA) copy of the RNA, isolated from the tissue of interest.
Hybridization between the substrate bound DNA and the analyte can be detected and quantitated by several means including but not limited to radioactive labeling or fluorescence labeling of the analyte or a secondary molecule designed to detect the hybrid. Quantitation of the level of gene expression can be done by comparison of the intensity of the signal from the analyte compared with that determined from known standards. The standards can be obtained by in vitro transcription of the target gene, quantitating the yield, and then using that material to generate a standard curve.

The above tests can be carried out on samples derived from a variety of patients' cells, bodily fluids and/or tissue extracts (homogenates or solubilized tissue) such as from tissue biopsy and autopsy material. Bodily fluids useful in the present invention include blood, urine, saliva, or any other bodily secretion or derivative thereof. Blood can include whole blood, plasma, serum, or any derivative of blood.



EXAMPLES
The present invention is further described by the following examples. These examples are provided solely to illustrate the invention by reference to specific embodiments. These exemplifications, while illustrating certain specific aspects of the invention, do not portray the limitations or circumscribe the scope of the disclosed invention.
Example 1
CSGs
Searches were carried out and CSGs identified using the following Search Tools as part of the LIFESEQ® database available from Incyte Pharmaceuticals, Palo Alto, Calif.:
1. Library Comparison (compares one library to one other library) allows the identification of clones expressed in tumor and absent or expressed at a lower level in normal tissue.
2. Subsetting is similar to library comparison but allows the identification of clones expressed in a pool of libraries and absent or expressed at a lower level in a second pool of libraries.
3. Transcript Imaging lists all of the clones in a single library or a pool of libraries based on abundance. Individual clones can then be examined using Electronic Northerns to determine the tissue sources of their component ESTs.
4. Protein Function: Incyte has identified subsets of ESTs with a potential protein function based on homologies to known proteins. Some examples in this database include Transcription Factors and Proteases. We identified some leads by searching in this database for clones whose component ESTs showed disease specificity.
Electronic subtractions, transcript imaging and protein function searches were used to identify clones, whose component ESTs were exclusively or more frequently found in libraries from specific tumors. Individual candidate clones were examined in detail by checking where each EST originated.







TABLE 1







CSGs










SEQ ID





NO:
Clone ID #
Gene ID #













1
238330
242807
Transcript Imaging


2
1285234
239588
Subsetting


3
1341701
29634
Transcript Imaging


4
816257
233421
Subsetting


5
775133
245080
Subsetting


6
1335450
245811
Subsetting


7
2348122
233711
Transcript Imaging


8
3228674
230273
Subsetting


9
1632174
229022
Transcript Imaging









The following example was carried out using standard techniques, which are well known and routine to those of skill in the art, except where otherwise described in detail. Routine molecular biology techniques of the following example can be carried out as described in standard laboratory manuals, such as Sambrook et al., MOLECULAR CLONING: A LABORATORY MANUAL, 2nd Ed.; Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989).
Example 2
Relative Quantitation of CSG Gene Expression
Real-Time quantitative PCR with fluorescent Taqman probes is a quantitation detection system utilizing the 5′-3′ nuclease activity of Taq DNA polymerase. The method uses an internal fluorescent oligonucleotide probe (Taqman) labeled with a 5′ reporter dye and a downstream, 3′ quencher dye. During PCR, the 5′-3′ nuclease activity of Taq DNA polymerase releases the reporter, whose fluorescence can then be detected by the laser detector of the Model 7700 Sequence Detection System (PE Applied Biosystems, Foster City, Calif., USA).
Amplification of an endogenous control is used to standardize the amount of sample RNA added to the reaction and normalize for Reverse Transcriptase (RT) efficiency. Either cyclophilin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) or 18S ribosomal RNA (rRNA) is used as this endogenous control. To calculate relative quantitation between all the samples studied, the target RNA levels for one sample are used as the basis for comparative results (calibrator). Quantitation relative to the “calibrator” can be obtained using the standard curve method or the comparative method (User Bulletin #2: ABI PRISM 7700 Sequence Detection System).
To evaluate the tissue distribution, and the level of CSGs in normal and tumor tissue, total RNA was extracted from normal tissues, tumor tissues, and from tumors and the corresponding matched normal tissues. Subsequently, first strand cDNA was prepared with reverse transcriptase and the polymerase chain reaction was done using primers and Taqman probe specific to the CSG. The results were analyzed using the ABI PRISM 7700 Sequence Detector. The absolute numbers are relative levels of expression of the CSG compared to the calibrator.
Comparative Examples
Similar mRNA expression analysis for genes coding for the diagnostic markers PSA (Prostate Specific Antigen) and PLA2 (Phospholipase A2) was performed for comparison. PSA is currently the only cancer screening marker available in clinical laboratories. When the panel of normal pooled tissues was analyzed, PSA was expressed at very high levels in prostate, with a very low expression in breast and testis. After analysis of more than 55 matching samples from 14 different tissues, the data corroborated the tissue specificity seen with normal tissue samples. PSA expression was compared in cancer and normal adjacent tissue for 12 matching samples of prostate tissue. The relative levels of PSA were higher in 10 cancer samples (83%). Clinical data recently obtained support the utilization of PLA2 as a staging marker for late stages of prostate cancer. mRNA expression data described herein showed overexpression of the mRNA in 8 out of the 12 prostate matching samples analyzed (66%). PLA2 had high levels of mRNA expression in small intestine, prostate, liver, and pancreas.
Measurement of SEQ ID NO:3; Clone ID 1341701; Gene ID 29634 (Cln106)
Absolute numbers are depicted in Table 2 as relative levels of expression of Cln106 (SEQ ID NO:3) in 12 normal different tissues. All the values are compared to normal testis (calibrator). These RNA samples are commercially available pools, originated by pooling samples of a particular tissue from different individuals.







TABLE 2







Relative levels of Cln106 Expression in Pooled


Samples










Tissue
NORMAL














Colon-Ascending
110



Endometrium
0



Kidney
0



Liver
0



Ovary
0



Pancreas
0



Prostate
16



Small Intestine
0



Spleen
0



Stomach
0



Testis
1



Uterus
0










The relative levels of expression in Table 2 show for the CSG Cln106 (SEQ ID NO:3), mRNA expression is more than 6 fold higher in the pool of normal ascending colon (110) compared with prostate (16). Testis, the calibrator, with a relative expression level of 1, is the only other tissue expressing the mRNA for Cln106 (SEQ ID NO:3). These results demonstrate that mRNA expression of this CSG is highly specific for colon.
The absolute numbers in Table 2 were obtained analyzing pools of samples of a particular tissue from different individuals. They can not be compared to the absolute numbers originated from RNA obtained from tissue samples of a single individual in Table 3.
The absolute numbers in Table 3 are relative levels of expression of Cln106 (SEQ ID NO:3) in 57 pairs of matching samples. All the values are compared to normal testis (calibrator). A matching pair is formed by mRNA from the cancer sample for a particular tissue and mRNA from the normal adjacent sample for that same tissue from the same individual.







TABLE 3







Relative levels of Cln106 Expression in Individual


Samples













Matching





Normal


Sample ID
Tissue
Cancer
Adjacent













Sto AC93
Stomach 1
4
96


Sto AC99
Stomach 2
0.4
0.5


Sml 21XA
Small Intestine 1
0
0


Sml H89
Small Intestine 2
0.93
1.28


Cln B56
Colon-Cecum (A) 1
317
101


Cln AS45
Colon-Ascending (A) 2
316.3
146.5


Cln CM67
Colon-Cecum (B) 3
481.0
217.5


Cln AS67
Colon-Ascending (B) 4
858.1
220.6


Cln AS43
Colon-Ascending (C) 5
1370
98


Cln AS46
Colon-Ascending (C) 6
3051
375


Cln AS98
Colon-Ascending (C) 7
26
42


Cln AS89
Colon-Ascending (D) 8
524.6
11.0


Cln TX01
Colon-Transverse (B) 9
2886.3
1992.0


Cln TX89
Colon-Transverse (B) 10
146.0
35.9


Cln TX67
Colon-Transverse (C) 11
2.9
421.7


Cln MT38
Colon-Splenic
1681
187



Flexture (M) 12


Cln SG89
Colon-Sigmoid (B) 13
1063.8
31.1


Cln SG67
Colon-Sigmoid (C) 14
8.5
9.4


Cln SG33
Colon-Sigmoid (C) 15
264
549


Cln SG45
Colon-Sigmoid (D) 16
580.0
114.6


Cln B34
Colon-Rectosigmoid (A) 17
97
244


Cln CXGA
Colon-Rectum (A) 18
45.1
273.4


Cln RC67
Colon-Rectum (B) 19
2.7
20.0


Cln C9XR
Colon-Rectosigmoid (C) 20
609
460


Cln RS45
Colon-Rectosigmoid (C) 21
472.8
144.0


Cln RC01
Colon-Rectum (C) 22
568
129


Cln RC89
Colon-Rectum (D) 23
4.6
322.91


Bld 46XK
Bladder 1
0.2
0


Bld 66X
Bladder 2
1
1


Bld 32XK
Bladder 3
0.0
0.0


Kid 126XD
Kidney 1
0
0


Kid 12XD
Kidney 2
0
0


Kid 5XD
Kidney 3
0.0
1.0


Kid 6XD
Kidney 4
0.0
0.0


Kid 106XD
Kidney 5
0.4
0.0


Liv 42X
Liver 1
0.0
0.0


Liv 15XA
Liver 2
0.0
0.0


Liv 94XA
Liver 3
0.0
0.0


Lng AC69
Lung 1
2
0


Lng BR94
Lung 2
0
0


Lng 47XQ
Lung 3
0
0


Mam 59X
Mammary Gland 1
0
0


Mam B011X
Mammary Gland 2
0
0


Mam A06X
Mammary Gland 3
0
0


Ovr 103X
Ovary 1
0.04
2.08


Ovr 130X
Ovary 2
0.1
2.76


Pan 71XL
Pancreas 1
4.08
0.1


Pan 82XP
Pancreas 2
0
0


Pro 12B
Prostate 1
0.3
0


Pro 23B
Prostate 2
3
4


Pro 13XB
Prostate 3
2
7


Pro 34B
Prostate 4
0.54
4.01


Pro 20XB
Prostate 5
4.8
4.3


Pro 65XB
Prostate 6
0.7
1.3


Tst 39X
Testis 1
2.78
0


End 8XA
Endometrium 1
0
0.2


Utr 85XU
Uterus 1
1.26
0





0 = Negative 






When matching samples were analyzed, the higher levels of expression were in the colon, showing a high degree of tissue specificity for this tissue. These results confirm the tissue specificity results obtained with the panel of normal pooled samples (Table 2). Furthermore, the level of mRNA expression in cancer samples and the isogenic normal adjacent tissue from the same individual were compared. This comparison provides an indication of specificity for the cancer stage (e.g. higher levels of mRNA expression in the cancer sample compared to the normal adjacent). Table 3 shows overexpression of Cln106 (SEQ ID NO:3) in 15 colon cancer tissues compared with their respective normal adjacent (colon samples #1, 2, 3, 4, 5, 6, 8, 9, 10, 12, 13, 16, 20, 21, and 22). There is overexpression in the cancer tissue for 65% of the colon matching samples tested (total of 23 colon matching samples). The matching sample Pan 71XL is a secondary cancer in pancreas, the primary cancer in that individual was a duodenal cancer.
Altogether, the high level of tissue specificity, plus the mRNA overexpression in 65% of the colon matching samples tested are demonstrative of CSG Cln106 (SEQ ID NO:3) being a diagnostic marker for colon cancer.
Measurement of SEQ ID NO:4; Clone ID 816257; Gene ID 406452 (Cln107)
Absolute numbers as depicted in Table 4 are relative levels of expression of CSG Cln107 (SEQ ID NO:4) in 12 normal different tissues. All the values are compared to normal small intestine (calibrator). These RNA samples are commercially available pools, originated by pooling samples of a particular tissue from different individuals.







TABLE 4







Relative levels of Cln107 Expression in Pooled


Samples










Tissue
NORMAL














Colon-Ascending
3.2



Endometrium
0



Kidney
0.2



Liver
0



Ovary
0



Pancreas
0



Prostate
0.1



Small Intestine
1



Spleen
0



Stomach
0.3



Testis
0



Uterus
0










The relative levels of expression in Table 4 show that mRNA expression of the CSG Cln107 (SEQ ID NO:4) is more than 10 fold higher in the pool of normal ascending colon (3.2), five fold higher in small intestine (1), and 1.5 fold higher in stomach (0.3), compared with the next higher expresser (0.2 for kidney). Seven of the pooled tissues samples analyzed were negative and prostate showed a relative expression of 0.1 for Cln107 (SEQ ID NO:4). These results demonstrate that Cln107 mRNA expression is highly specific for colon, small intestine, and in a lower degree for stomach.
The absolute numbers in Table 4 were obtained analyzing pools of samples of a particular tissue from different individuals. They can not be compared to the absolute numbers originated from RNA obtained from tissue samples of a single individual in Table 5.
The absolute numbers in Table 5 are relative levels of expression of Cln107 (SEQ ID NO:4) in 57 pairs of matching samples. All the values are compared to normal small intestine (calibrator). A matching pair is formed by mRNA from the cancer sample for a particular tissue and mRNA from the normal adjacent sample for that same tissue from the same individual.







TABLE 5







Relative levels of Cln107 Expression in Individual


Samples













Matching





Normal


Sample ID
Tissue
Cancer
Adjacent













Sto AC93
Stomach 1
8.9
13.4


Sto AC99
Stomach 2
6.0
0.9


Sml 21XA
Small Intestine 1
1.07
1.42


Sml H89
Small Intestine 2
0.97
4.13


Cln B56
Colon-Cecum (A) 1
2
16


Cln AS45
Colon-Ascending (A) 2
0.7
2.1


Cln CM67
Colon-Cecum (B) 3
1.6
2.1


Cln AS67
Colon-Ascending (B) 4
1.2
6.2


Cln AS43
Colon-Ascending (C) 5
13.5
0.5


Cln AS46
Colon-Ascending (C) 6
9.7
23.6


Cln AS98
Colon-Ascending (C) 7
28.1
1.4


Cln AS89
Colon-Ascending (D) 8
0.9
3.1


Cln TX01
Colon-Transverse (B) 9
3.0
10.6


Cln TX89
Colon-Transverse (B) 10
4.5
0.6


Cln TX67
Colon-Transverse (C) 11
3.6
3.4


Cln MT38
Colon-Splenic
4.0
2.6



Flexture (M) 12


Cln SG89
Colon-Sigmoid (B) 13
4.7
0.9


Cln SG67
Colon-Sigmoid (C) 14
1.0
1.3


Cln SG33
Colon-Sigmoid (C) 15
14.2
7.6


Cln SG45
Colon-Sigmoid (D) 16
4.8
6.0


Cln B34
Colon-Rectosigmoid (A) 17
3
2


Cln CXGA
Colon-Rectum (A) 18
4.4
1.9


Cln RC67
Colon-Rectum (B) 19
0.1
0.4


Cln C9XR
Colon-Rectosigmoid (C) 20
5
3


Cln RS45
Colon-Rectosigmoid (C) 21
11.4
4.6


Cln RC01
Colon-Rectum (C) 22
1.8
2.3


Cln RC89
Colon-Rectum (D) 23
0.1
5.35


Bld 46XK
Bladder 1
0.2
0


Bld 66X
Bladder 2
1
1


Bld 32XK
Bladder 3
0.1
0.1


Kid 126XD
Kidney 1
0
0.02


Kid 12XD
Kidney 2
0.1
0.2


Kid 5XD
Kidney 3
0.3
0.0


Kid 6XD
Kidney 4
0.1
0.1


Kid 106XD
Kidney 5
0.0
0.1


Liv 42X
Liver 1
7.9
0.002


Liv 15XA
Liver 2
0.0
0.0


Liv 94XA
Liver 3
0.0
0.0


Lng AC69
Lung 1
1.6
0.2


Lng BR94
Lung 2
0.4
0


Lng 47XQ
Lung 3
0.78
0.2


Mam 59X
Mammary Gland 1
0.05
0.3


Mam B011X
Mammary Gland 2
0.01
0.004


Mam A06X
Mammary Gland 3
0.22
0


Ovr 103X
Ovary 1
0.01
0.01


Ovr 130X
Ovary 2
0.09
0.1


Pan 71XL
Pancreas 1
2.51
2.81


Pan 82XP
Pancreas 2
0
0.62


Pro 12B
Prostate 1
0.3
0.1


Pro 23B
Prostate 2
0.3
0.2


Pro 13XB
Prostate 3
0
0


Pro 34B
Prostate 4
0.04
0.22


Pro 20XB
Prostate 5
0.4
0.1


Pro 65XB
Prostate 6
0.0
0.1


Tst 39X
Testis 1
0.02
0.01


End 8XA
Endometrium 1
0.01
0.5


Utr 85XU
Uterus 1
0.03
0





0 = Negative 






When matching samples were analyzed, the higher levels of expression were in colon, stomach, and small intestine, showing a high degree of tissue specificity for colon tissues. These results confirm the tissue specificity results obtained with normal pooled samples (Table 4). Furthermore, the level of mRNA expression in cancer samples and the isogenic normal adjacent tissue from the same individual were compared. This comparison provides an indication of specificity for the cancer stage (e.g. higher levels of mRNA expression in the cancer sample compared to the normal adjacent). Table 5 shows overexpression of Cln107 (SEQ ID NO:4) in 11 colon cancer tissues compared with their respective normal adjacent (colon samples #5, 7, 10, 11, 12, 13, 15, 17, 18, 20, and 21). There is overexpression in the cancer tissue for 48% of the colon matching samples tested (total of 23 colon matching samples). The matching sample Pan 71XL is a secondary cancer in pancreas, the primary cancer in that individual was a duodenal cancer.
Altogether, the high level of tissue specificity, plus the mRNA overexpression in almost half of the colon, stomach, and small intestine matching samples tested are demonstrative of CSG Cln107 (SEQ ID NO:4) being a diagnostic marker for colon cancer.
Measurement of SEQ ID NO:5; Clone ID 775133; Gene ID 24508 (Cln108)
The absolute numbers shown in Table 6 are relative levels of expression of CSG Cln108 (SEQ ID NO:5) in 12 normal different tissues. All the values are compared to normal small intestine (calibrator). These RNA samples are commercially available pools, originated by pooling samples of a particular tissue from different individuals.







TABLE 6







Relative levels of Cln108 Expression in Pooled


Samples










Tissue
NORMAL














Colon-Ascending
2846.5



Endometrium
1



Kidney
5.5



Liver
18.7



Ovary
3.4



Pancreas
198.1



Prostate
1024



Small Intestine
810.8



Spleen
32.2



Stomach
9981.2



Testis
0



Uterus
294.1










The relative levels of expression in Table 6 show that mRNA expression of CSG Cln108 (SEQ ID NO:5) is more than 10 fold higher in the pool of normal ascending colon (2846.5) and almost ten fold higher in stomach (9981.2), compared to the expression level in any other tissue analyzed. These results demonstrate that mRNA expression of this CSG is also highly specific for colon and stomach.

The absolute numbers in Table 6 were obtained analyzing pools of samples of a particular tissue from different individuals. They can not be compared to the absolute numbers originated from RNA obtained from tissue samples of a single individual in Table 7.
The absolute numbers depicted in Table 7 are relative levels of expression of Cln108 (SEQ ID NO:5) in 57 pairs of matching samples. All the values are compared to normal small intestine (calibrator). A matching pair is formed by mRNA from the cancer sample for a particular tissue and mRNA from the normal adjacent sample for that same tissue from the same individual.







TABLE 7







Relative levels of Cln108 Expression in Individual


Samples













Matching





Normal


Sample ID
Tissue
Cancer
Adjacent













Sto AC93
Stomach 1
28696
34842


Sto AC99
Stomach 2
21523
30862


Sml 21XA
Small Intestine 1
2944
964.4


Sml H89
Small Intestine 2
244.5
3513.2


Cln B56
Colon-Cecum (A) 1
27242
24637


Cln AS45
Colon-Ascending (A) 2
5827.0
8771.0


Cln CM67
Colon-Cecum (B) 3
4251.0
4684.0


Cln AS67
Colon-Ascending (B) 4
564.0
1949.0


Cln AS43
Colon-Ascending (C) 5
50310
10949


Cln AS46
Colon-Ascending (C) 6
246044
120073


Cln AS98
Colon-Ascending (C) 7
40442
17482


Cln AS89
Colon-Ascending (D) 8
5730.0
1581.0


Cln TX01
Colon-Transverse (B) 9
22281.0
114784.0


Cln TX89
Colon-Transverse (B) 10
11026.0
1639.0


Cln TX67
Colon-Transverse (C) 11
17004.0
11654.0


Cln MT38
Colon-Splenic
77589
31620



Flexture (M) 12


Cln SG89
Colon-Sigmoid (B) 13
140339.0
49617.0


Cln SG67
Colon-Sigmoid (C) 14
4951.0
7905.0


Cln SG33
Colon-Sigmoid (C) 15
60875
120490


Cln SG45
Colon-Sigmoid (D) 16
30437.0
47267.0


Cln B34
Colon-Rectosigmoid (A) 17
5848
5861


Cln CXGA
Colon-Rectum (A) 18
13877.0
9787.0


Cln RC67
Colon-Rectum (B) 19
1703.0
26589.0


Cln C9XR
Colon-Rectosigmoid (C) 20
2458
19071


Cln RS45
Colon-Rectosigmoid (C) 21
95523
61939


Cln RC01
Colon-Rectum (C) 22
98891.0
80047.0


Cln RC89
Colon-Rectum (D) 23
17.0
1775


Bld 46XK
Bladder 1
0
8


Bld 66X
Bladder 2
397
44


Bld 32XK
Bladder 3
0.0
16.0


Kid 126XD
Kidney 1
32
22


Kid 12XD
Kidney 2
6
0


Kid 106XD
Kidney 3
4.0
33.0


Liv 42X
Liver 1
4783
0


Liv 15XA
Liver 2
4.0
10.0


Liv 94XA
Liver 3
159.0
21.0


Lng AC69
Lung 1
222
295


Lng BR94
Lung 2
112
0


Lng 47XQ
Lung 3
30
69


Lng AC66
Lung 4
29
137


Mam 59X
Mammary Gland 1
56
0


Mam B011X
Mammary Gland 2
54
31


Mam A06X
Mammary Gland 3
12
0


Ovr 103X
Ovary 1
37
0


Pan 71XL
Pancreas 1
13203
4163


Pan 82XP
Pancreas 2
39.1
0


Pro 12B
Prostate 1
386
88


Pro 23B
Prostate 2
250
23


Pro 13XB
Prostate 3
92
731


Pro 34B
Prostate 4
33.3
265.7


Pro 20XB
Prostate 5
454.6
1908.9


Pro 65XB
Prostate 6
733.5
922.0


End 8XA
Endometrium 1
5
92


Utr 85XU
Uterus 1
98.9
21.8


Utr 23XU
Uterus 2
35.3
0


Utr 135XO
Uterus 3
39.2
43.8


Utr 141XO
Uterus 4
212.1
55.9





0 = Negative 






When matching samples were analyzed, the higher levels of expression were in colon and stomach, showing a high degree of tissue specificity for these two tissues. These results confirm the tissue specificity results obtained with normal pooled samples (Table 6). Furthermore, the level of mRNA expression in cancer samples and the isogenic normal adjacent tissue from the same individual were compared. This comparison provides an indication of specificity for the cancer stage (e.g. higher levels of mRNA expression in the cancer sample compared to the normal adjacent). Table 7 shows overexpression of CSG Cln108 (SEQ ID NO:5) in 13 colon cancer tissues compared with their respective normal adjacent (colon samples #1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 21, and 22). There is overexpression in the cancer tissue for 56% of the colon matching samples tested (total of 23 colon matching samples). The matching sample Pan 71XL is a secondary cancer in pancreas, the primary cancer in that individual was a duodenal cancer.
Altogether, the high level of tissue specificity, plus the mRNA overexpression in more than half of the colon, stomach, and small intestine matching samples tested are demonstrative of this CSG, Cln108 (SEQ ID NO:5), also being a diagnostic marker for colon cancer.
Measurement of SEQ ID NO:7; Clone ID 2348122; Gene ID 23371 (Cln109)
The absolute numbers depicted in Table 8 are relative levels of expression of CSG Cln109 (SEQ ID NO:7) in 12 normal different tissues. All the values are compared to normal ovary (calibrator). These RNA samples are commercially available pools, originated by pooling samples of a particular tissue from different individuals.







TABLE 8







Relative levels of Cln109 Expression in Pooled


Samples










Tissue
NORMAL














Colon-Ascending
28.8



Endometrium
0.45



Kidney
0.41



Liver
0.72



Ovary
0.07



Pancreas
82.8



Prostate
124.3



Small Intestine
626.4



Spleen
1.2



Stomach
12.05



Testis
1.51



Uterus
52.99










The relative levels of expression in Table 8 show that mRNA expression of CSG Cln109 (SEQ ID NO:7), is more than 5 fold higher in the pool of normal small intestine (626.4) compared to the expression level in any other tissue analyzed. These results demonstrate that Cln109 (SEQ ID NO:7) mRNA expression is highly specific for small intestine.

The absolute numbers in Table 8 were obtained analyzing pools of samples of a particular tissue from different individuals. They can not be compared to the absolute numbers originated from RNA obtained from tissue samples of a single individual in Table 9.
The absolute numbers depicted in Table 9 are relative levels of expression of Cln109 (SEQ ID NO:7) in 53 pairs of matching samples. All the values are compared to normal ovary (calibrator). A matching pair is formed by mRNA from the cancer sample for a particular tissue and mRNA from the normal adjacent sample for that same tissue from the same individual.







TABLE 9







Relative levels of Cln109 Expression in Individual


Samples













Matching





Normal


Sample ID
Tissue
Cancer
Adjacent













Sto AC93
Stomach 1
2574
1310


Sto AC99
Stomach 2
4153
5


Sml 21XA
Small Intestine 1
2667
13663.8


Sml H89
Small Intestine 2
57.8
904.29


Cln B56
Colon-Cecum (A) 1
6794
299


Cln AS45
Colon-Ascending (A) 2
814.6
105.8


Cln CM67
Colon-Cecum (B) 3
294.6
36.1


Cln AS67
Colon-Ascending (B) 4
2.2
26.3


Cln AS43
Colon-Ascending (C) 5
111
377


Cln AS46
Colon-Ascending (C) 6
1180
352


Cln AS98
Colon-Ascending (C) 7
1075
92


Cln AS89
Colon-Ascending (D) 8
14022.7
87.5


Cln TX01
Colon-Transverse (B) 9
1027.6
282.1


Cln TX89
Colon-Transverse (B) 10
2.5
23.7


Cln TX67
Colon-Transverse (C) 11
0.1
72.3


Cln MT38
Colon-Splenic
372
88



Flexture (M) 12


Cln SG89
Colon-Sigmoid (B) 13
179.2
33.4


Cln SG67
Colon-Sigmoid (C) 14
85.0
94.7


Cln SG33
Colon-Sigmoid (C) 15
5461
377


Cln SG45
Colon-Sigmoid (D) 16
762.7
15.9


Cln B34
Colon-Rectosigmoid (A) 17
460
1


Cln RC67
Colon-Rectum (B) 18
64.5
136.2


Cln C9XR
Colon-Rectosigmoid (C) 19
441
34


Cln RS45
Colon-Rectosigmoid (C) 20
1931
195


Cln RC01
Colon-Rectum (C) 21
72.8
19.1


Cln RC89
Colon-Rectum (D) 22
4.8
90.2


Bld 46XK
Bladder 1
4
3


Bld 66X
Bladder 2
1
0


Bld 32XK
Bladder 3
0.1
307.6


Kid 126XD
Kidney 1
0
2


Kid 12XD
Kidney 2
3
16


Kid 5XD
Kidney 3
0.0
0.3


Kid 6XD
Kidney 4
18.5
1.2


Liv 42X
Liver 1
21
0.03


Liv 15XA
Liver 2
0.5
0.4


Liv 94XA
Liver 3
0.4
0.0


Lng AC69
Lung 1
0.1
0


Lng BR94
Lung 2
3
0


Lng 60XL
Lung 3
0.1
0


Mam 59X
Mammary Gland 1
0
4


Mam B011X
Mammary Gland 2
8
13


Mam A06X
Mammary Gland 3
4.7
9.6


Pan 71XL
Pancreas 1
8902.5
1428.2


Pan 82XP
Pancreas 2
0.2
9.3


Pro 12B
Prostate 1
9
20


Pro 23B
Prostate 2
191
88


Pro 13XB
Prostate 3
12
460


Pro 34B
Prostate 4
3.2
80.4


Tst 39X
Testis 1
29.9
0


End 8XA
Endometrium 1
0.3
21


Utr 85XU
Uterus 1
244.7
592.2


Ovr 63A
Ovary 1
11.4
0


Ovr A1C
Ovary 2
68.4
0





0 = Negative 






When matching samples were analyzed, the higher levels of expression were in small intestine, colon and stomach, showing a high degree of tissue specificity for these three colon tissues. These results confirm the tissue specificity results obtained with normal pooled samples for small intestine (Table 8). Furthermore, the level of mRNA expression in cancer samples and the isogenic normal adjacent tissue from the same individual were compared. This comparison provides an indication of specificity for the cancer stage (e.g. higher levels of mRNA expression in the cancer sample compared to the normal adjacent). Table 9 shows overexpression of CSG, Cln109 (SEQ ID NO:7) in 15 colon cancer tissues compared with their respective normal adjacent (colon samples #1, 2, 3, 6, 7, 8, 9, 12, 13, 15, 16, 17, 19, 20, and 21). There is overexpression in the cancer tissue for 68% of the colon matching samples tested (total of 22 colon matching samples). The matching sample Pan 71XL is a secondary cancer in pancreas, the primary cancer in that individual was a duodenal cancer.
Altogether, the high level of tissue specificity, plus the mRNA overexpression in more than half of the colon, stomach, and small intestine matching samples tested are demonstrative of CSG Cln109 (SEQ ID NO:7) being a diagnostic marker for colon cancer. The amino acid sequence encoded by the open reading frame of Cln109 is depicted in SEQ ID NO:10.

## Claims

1. A method for detecting colon cancer in a patient comprising:
(a) measuring levels of a polynucleotide comprising SEQ ID NO:3 or native protein encoded by SEQ ID NO:3 in a sample of cells, tissue or bodily fluid obtained from the patient; and 
(b) comparing the measured levels of the polynucleotide comprising SEQ ID NO:3 or the native protein encoded by SEQ ID NO:3 with levels of the polynucleotide comprising SEQ ID NO:3 or the native protein encoded by SEQ ID NO:3 in a sample of cells, tissue or bodily fluid obtained from a control, wherein an increase in measured levels of the polynucleotide comprising SEQ ID NO:3 or the native protein encoded by SEQ ID NO:3 in the patient versus the levels of the polynucleotide comprising SEQ ID NO:3 or the native protein encoded by SEQ ID NO:3 in the control is associated with the presence of colon cancer.

2. The method of claim 1 wherein the sample is cells.

3. The method of claim 1 wherein the sample is tissues.

4. The method of claim 1 wherein the sample is bodily fluids.

5. The method of claim 1 wherein levels of the polynucleotide comprising SEQ ID NO:3 are measured.

6. The method of claim 5 wherein the sample is cells.

7. The method of claim 5 wherein the sample is tissues.

8. The method of claim 5 wherein the sample is bodily fluids.

9. The method of claim 1 wherein levels of the native protein encoded by SEQ ID NO:3 are measured.

10. The method of claim 9 wherein the sample is cells.

11. The method of claim 9 wherein the sample is tissues.

12. The method of claim 9 wherein the sample is bodily fluids.