CA2345000A1 - A novel method of diagnosing, monitoring, staging, imaging and treating gastrointestinal cancers - Google Patents
A novel method of diagnosing, monitoring, staging, imaging and treating gastrointestinal cancers Download PDFInfo
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Abstract
The present invention provides a new method for detecting, diagnosing, monitoring, staging, prognosticating, imaging and treating gastrointestinal cancers including small intestine, colon and stomach cancer.
Description
A NOVEL METHOD OF DIAGNOSING, MONITORING, STAGING, IMAGING AND '.PREATING GASTROINTESTINAL CANCERS
FIELD OF THE INVENTION
This invention relates, in part, to newly developed assays for detecting, diagnosing, monitoring, staging prognosticating, imaging and treating cancers, particularly gastrointestinal cancers including cancer of the stomach, small intestine and colon.
BACKGROUND OF THE INVENTION
Cancer of the colon is the second most frequently diagnosed malignancy in the United States, as well as the second most common cause of cancer death. Colon cancer is a highly treatable and often curable disease when localized to the bowel. Surgery is the primary treatment and results in cure in approximately 50°s of patients. However, recurrence and metastases following surgery is a major problem and often is the ultimate cause of death.
Due to its proximity, cancer of the colon often metastasizes to the small intestine. The prognosis of the cancer spreading to the small intestine is 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 colon cancer. Various characteristics also assist in prognosticating colon cancer arid its spread to the small intestines. For example, bowel obstruction and bowel perforation are indicators of poor prognosis.
Elevated pretreatment serum levels of carcinoembryonic antigen (CEA) and of carbohydrate antigen 19-9 (CA 19-9) also have a negative prognostic significance. However, age greater than 70 years at presentation is not a contraindication to standard therapies; acceptable morbidity and mortality, as well as long-term survival, are achieved in this patient population.
Cancer cells can also originate in the small intestine. However, this :is a much rarer type of cancer.
Symptoms of cancer of the small intestine typically include pain or cramps in the middle of the abdomen, weight loss without dieting, a lump in the abdomen or blood in the stool.
Cancer of the stomach, also referred to as gastric cancer, also frequently metastasizes to the small intestine due to its proximity. This cancer is often difficult to diagnose in early stages and can be in the stomach for a long time, growing to a large size before symptoms arise.
In the early stages of cancer of the stomach, an individual may experience indigestion and stomach discomfort, a bloated feeling after' eating, mild nausea, loss of appetite or heartburn. In more advanced stages of stomach cancer, there may be blood in. the stool, vomiting, weight loss or more severe pain.
Because of the frequency of these types of cancer (approximately 160,000 new cases of colon and rectal cancer per year alone), the identification of high-risk groups, the demonstrated slow growth of primary lesions and the better survival of early-stage lesions, screening for gastrointestinal cancers 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 cancer of the colon, small intestine or stomach are of critical importance to the outcome of the patient. Patients diagnosed with early stage cancer generally have a much greater five-year survival rate as compared to the survival rate for patients diagnosed with distant metastasized cancers. New diagnostic methods which are more sensitive and specific for detecting early cancer of the stomach, small intestine and colon are clearly needed.
Patients with gastrointestinal cancers are closely monitored following initial therapy and during adjuvant therapy to determine response t:o therapy and to detect persistent or recurrent disease of metastasis. There is clearly a need for a cancer' marker which is more sensitive and specific in detecting recurrence of these types of cancer.
Another important step in managing gastrointestinal cancers is to determine the stage of the patient's disease.
Stage determination has potential prognostic value and provides criteria for designing optimal therapy.
Generally, pathological staging of cancer is preferable over clinical staging because the former gives a more accurate prognosis. However, clinical staging would be preferred were it at least as accurate as pathological staging because it does not depend on an invasive procedure to obtain tissue for pathological evaluation. Staging of gastrointestinal cancers would be improved by identifying new markers in cells, tissues, or bodily fluids which could differentiate between different stages of invasion.
Thirteen colon specific genes and naturally occurring variants thereof, referred to as CSGl-13, are disclosed in U.S. Patent 5,733,748 and WO 96/39541 for use as diagnostic markers in colon cancer. Some of these genes and polypeptides encoded thereby are also taught to be useful in determining if the colon cancer has metastasized.
U.S. Patent 5,,861,494, which issued January 19, 1999, also discloses a gene and polypeptide encoded thereby for use as a diagnostic marker for colon cancer and as an agent for determining if t:he colon cancer has metastasized. This gene and the polypeptide encoded thereby are similar in sequence to the cancer specific gene referred to herein as CC2.
It has now been found that CC2 is a useful diagnostic and metastatic marker not only for colon cancer but also for cancer of the stomach and small intestine. Thus, in the present invention,,, methods are provided for detecting, diagnosing, monitoring, staging, prognosticating, imaging and treating gastrointestinal cancers including cancer of the stomach, small intestine and colon via the cancer specific gene referred to herein as CC2. CC2 refers, among other things, to native protein expressed by the gene comprising the polynuc:leotide sequence of SEQ ID N0:1. The amino acid sequence oi: a polypeptide encoded by SEQ ID NO:1 is depicted herein as SEQ ID N0:2. In the alternative, what is meant by CC2 as used herein, means the native mRNA
encoded by the gene comprising the polynucleotide sequence of SEQ ID NO:1 or levels of the gene comprising the polynucleotide sequence of SEQ ID N0:1.
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.
SUi~IARY 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 a gastrointestinal cancer by analyzing for changes in levels of CC2 in cells, tissues or bodily fluids compared with levels. of CC2 in preferably the same cells, tissues, or bodily fluid type of a normal human control, wherein a change in levels of CC2 in the patient versus the normal human control is associated with a gastrointestinal cancer.
Further provided is a method of diagnosing metastatic cancer in a patient having a gastrointestinal cancer which is not known to have metastasized by identifying a human patient suspected of having a gastrointestinal cancer that has metastasized; analyzing a sample of cells, tissues, or bodily fluid from such patient for CC2; comparing the CC2 levels in such cells, tissues, or bodily fluid with levels of CC2 in preferably the same cells, tissues, or bodily fluid type of a normal human control, wherein an increase in CC2 levels in the patient versus the normal human control is associated with a gastrointestinal cancer which has metastasized.
Also provided by the invention is a method of staging a gastrointestinal cancer in a human which has such cancer by identifying a human patient having such cancer;
analyzing a sample of_ cells, tissues, or bodily fluid from such patient for CC2; comparing CC2 levels in such cells, tissues, or bodily f)._uid with levels of CC2 in preferably the same cells, tis:>ues, or bodily fluid type of a normal human control sample, wherein an increase in CC2 levels in the patient versus the normal human control is associated with a cancer which is progressing and a decrease in the levels of CC2 is as:>ociated with a cancer which is regressing or in remission.
Further provided is a method of monitoring a gastrointestinal 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 CC2;
comparing the CC2 levels in such cells, tissue, or bodily fluid with levels o:E CC2 in preferably the same cells, tissues, or bodily fluid type of a normal human control sample, wherein an increase in CC2 levels in the patient versus the normal human control is associated with a cancer which has metastasized.
Further provided is a method of monitoring the change in stage of a gastrointestinal cancer in a human having such cancer by looking at levels of CC2 in a human having such cancer. The method comprises identifying a human patient having such cancer; periodically analyzing a sample of cells, tissues, o:r bodily fluid from such patient for CC2; comparing the CC2 levels in such cells, tissue, or bodily fluid with levels of CC2 in preferably the same cells, tissues, or bodily fluid type of a normal human control sample, wherein an increase in CC2 levels in the patient versus the normal human control is associated with a cancer which is progressing and a decrease in the levels of CC2 is associated with a cancer which is regressing or in remission.
Further provided are antibodies targeted against CC2 or fragments of such antibodies which can be used to detect or image localization of CC2 in a patient for the purpose of detecting or diagnosing a disease or condition. Such antibodies can be polyclonal, monoclonal, or omniclonal or prepared by molecular biology techniques. The term "antibody", as used herein and throughout the instant specification is also meant to include aptamers and single-stranded oligonucleotides such as those derived from an in vitro evolution protocol referred to as SELEX and well known to those skilled in the art. Antibodies can be labeled with a variety of detectable labels including, but not limited to, radioisotopes and paramagnetic metals.
These antibodies or_ f:ragments thereof can also be used as therapeutic agents in the treatment of diseases characterized by expression of CC2. In therapeutic applications, the antibody can be used without or with derivatization to a cytotoxic agent such as a radioisotope, enzyme, toxin, drug or a prodrug.
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, ar~a 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.
DETAILED 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 CC2 with those of CC2 in a normal human control. What is meant by levels of CC2 as used herein, means levels of the native protein expressed by the gene comprising the pol.ynucleotide sequence of SEQ ID N0:1.
The amino acid sequence of a polypeptide encoded by SEQ ID
NO:l is depicted herein as SEQ ID N0:2. In the alternative, what is meant by levels of CC2 as used herein, means levels of the 'native mRNA encoded by the gene comprising the polynucleotide sequence of SEQ ID N0:1 or levels of the gene comprising t:he polynucleotide sequence of SEQ ID NO:l. 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 overexpression of CC2 protein compared to normal control bodily fluids, cells, or tissue samples may be used to diagnose the presence of cancers, _ g _ and in particular gastrointestinal cancers. By gastrointestinal cancers it. is meant to include stomach cancer, cancer of the small intestine, and colon cancer.
All the methods of: the present invention may optionally include measuring levels of other cancer markers as well as CC2. Other cancer markers, in addition to CC2, useful in the present invention will depend on the cancer being tested and are known to those of skill in the art.
Diagnostic Asssys The present inv~antion provides methods for diagnosing the presence of a gastrointestinal cancer by analyzing for changes in levels of CC2 in cells, tissues or bodily fluids compared with levels of CC2 in cells, tissues or bodily fluids of preferably the same type from a normal human control, wherein a clnange in levels of CC2 in the patient versus the normal human control is associated with the presence of a gastrointestinal cancer.
Without limiting the instant invention, typically, for a quantitative diagnostic assay a positive result indicating the patient being tested has cancer is one in which cells, tissues or bodily fluid levels of the cancer marker, such as CC2, 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 the onset of metastatic gastrointestinal cancers in a patient having a gastrointestinal cancer which has not yet metastasized. In the method of the present invention, a human cancer patient suspected of having a gastrointestinal 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.
_ g _ In the present. invention, determining the presence of CC2 levels in cells, tissues or bodily fluid, is particularly useful for discriminating between gastrointestinal cancers which have not metastasized and gastrointestinal cancers which have metastasized. Existing techniques have difficulty discriminating between gastrointestinal cancers which have metastasized and gastrointestinal cancers which have not metastasized.
However, proper treatment selection is often dependent upon such knowledge.
In the present invention, the cancer marker level measured in cells, tissues or bodily fluid of a human patient is CC2. The measured CC2 level in the human patient is compared 'with levels of CC2_ in preferably the same cells, tissue or bodily fluid type of a normal human control. That is, if the cancer marker being observed is CC2 in serum, this level is preferably compared with the level of CC2 in serum of a normal human control. An increase in the CC2 in the patient versus the normal human control is associated with a gastrointestinal cancer which has metastasized.
Without l.imiti.ng the instant invention, typically, for a quantitative diagnostic assay a positive result indicating the cancer i.n the patient being tested or monitored has metastasized is one in which cells, tissues or bodily fluid levels of the cancer marker, such as CC2, are at least two times higher, and most preferably are at least five times higher, than i.n 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 preferably also include samples from a human patient that is determined by reliable methods to have a gastrointestinal cancer which has not metastasized.
Staging The invention also provides a method of staging gastrointestinal cancers in a human patient. The method comprises identifying a human patient having such cancer and analyzing a samplfs of cells, tissues or bodily fluid from such human patient for CC2. In this method CC2 levels in such cells, tissues or bodily fluid are then compared with levels of CC2 in preferably the same cells, tissues or bodily fluid type of a normal human control sample, wherein an increase in CC2 levels in the human patient versus the normal human control _is associated with a cancer which is progressing and a decrease in the levels of CC2 is associated with a cancer which is regressing or in remission.
Monitoring Further provided is a method of monitoring gastrointestinal cancers 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 human. patient for CC2; comparing the CC2 levels in such cells, tissues or bodily fluid with levels of CC2 in preferably the same cells, tissues or bodily fluid type of a normal human control, wherein an :increase in CC2 levels in the human patient versus the normal human control is associated with a cancer which has metastasized.
Further provided by this invention is a method of monitoring the change in stage of gastrointestinal cancers in a human having suwh cancer. The method comprises identifying a human patient having such cancer;
periodically analyzing a sample of cells, tissues or bodily fluid from such human patient for CC2; and comparing the ' CC2 levels in such cells, tissues or bodily fluid with levels of CC2 in preferably the same cells, tissues or bodily fluid type of a normal human control, wherein an increase in CC2 levels in the human patient versus the normal human control is associated with a cancer which is progressing in stage and a decrease in the levels of CC2 is associated with a cancer which is regressing in stage or in remission.
Monitoring such patient for onset of metastasis is periodic and preferalaly 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 (:including protein levels), such as CC2 of the present invention, in a sample derived from a patient are well known to those of skill in the art. Such assay methods include, without limitation, radioimmunoassays, reverse transcriptase PCR (RT-PCR) assays, immunohistoclnemistry assays, in situ hybridization assays, competitive-binding assays, Western Blot analyses, ELISA assays and proteomic approaches: two-dimensional gel electrophoresis (2D ~alectrophox~esis) and non-gel based approaches such as mass spectrometry or protein interaction profiling. 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 CC2, preferably a monoclonal antibody.
In addition a reporter antibody generally is prepared which binds specifically to CC2. 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 CC2 is incubated on a solid support, e.g. a polystyrene dish, that binds the antibody. Any free protein binding sites an 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 tame CC2 binds to the specific antibody attached to the polystyrene dish. Unbound sample is washed out with buffer. A reporter antibody specifically directed to CC2 and linked to horseradish peroxidase is placed in the dish resulting in binding of the reporter antibody to any monoclonal antibody bound to CC2. Unattached reporter antibody is then washed out. Reagents for peroxidase activity, including a coiorimetric substrate are then added to the dish.
Immobilized peroxidase, linked to CC2 antibodies, produces a colored reaction product. The amount of color developed in a given time period is proportional to the amount of_ CC2 protein present in the sample. Quantitative results typically are obtained by reference to a standard curve.
A competition assay can also be employed wherein antibodies specific 'to CC2 are attached to a solid support and labeled CC2 and a sample derived from the host are passed over the solid support. The amount of label detected which is attached to the solid support can be correlated to a quantity of CC2 in the sample.
Nucleic acid methods can also be used to detect CC2 mRNA as a marker for gastrointestinal cancers. 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 thausands of other mRNA species. In RT-PC:R, 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 detect both the expression of and quantitate the level of expression of a gene. In this approach, a cDNA encoding the CC2 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 CC2 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 irucluding 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.
Of the proteornic approaches, 2D electrophoresis is a technique well known to those in the art. Isolation of individual proteins from a sample such as serum is accomplished using sequential separation of proteins by different characteristics usually on polyacrylamide gels.
First, proteins are separated by size using an electric current. The current acts uniformly on all proteins, so smaller proteins move farther on the gel than larger proteins. The second dimension applies a current perpendicular to the first and separates proteins not on the basis of size but an the specific electric charge carried by each protein. Since no two proteins with different sequences are identical on the basis of both size and charge, the result of a 2D separation is a square gel in which each protein accupies a unique spot. Analysis of the spots with chemical or antibody probes, or subsequent protein microsequencing can reveal the relative abundance of a given protein a:nd the identity of the proteins in the sample.
The above tests can be carried out on samples derived from a variety of cells, bodily fluids and/or tissue extracts (homogenates or solubilized tissue) obtained from a patient including 'those from tissue biopsies 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.
In Vivo Antibody Use Antibodies which specifically bind to CC2 can also be used in vivo in patients suspected of suffering from gastrointestinal cancers including stomach cancer, cancer of the small intestine, and colon cancer. Specifically, antibodies which specifically bind a CC2 can be injected into a patient suspected of having a gastrointestinal cancer for diagnostic and/or therapeutic purposes. The preparation and use of antibodies for in vivo diagnosis is well known in the art. For example, antibody-chelators labeled with Indium-111 have been described for use in the radioimmunoscintographi.c imaging of carcinoembryonic antigen expressing tumors (Sumerdon et al. Nucl. Med. Biol.
1990 17:247-254). I:n particular, these antibody-chelators have been used in detecting tumors in patients suspected of having recurrent colorectal cancer (Griffin et al. J. Clin.
Onc. 1991 9:631-640).. Antibodies with paramagnetic ions as labels for use in magnetic resonance imaging have also been described (Lauffer, R.B. Magnetic Resonance in Medicine 1991 22:339-342). Antibodies directed against CC2 can be used in a similar manner. Labeled antibodies which specifically bind CCa? can be injected into patients suspected of having a gastrointestinal cancer for the purpose of diagnosing or staging of the disease status of the patient. The label used will be selected in accordance with the imaging modality to be used. For example, radioactive labels such as Indium-111, Technetium-99m or Iodine-131 can be usE~d for planar scans or single photon emission computed tornography (SPELT). Positron emitting labels such as Fluor~~ne-19 can be used in positron emission tomography. Paramagnetic ions such as Gadlinium (III) or Manganese (II) can be' used in magnetic resonance imaging (MRI). Localization of the label permits determination of the spread of the cancer. The amount of label within an organ or tissue also allows determination of the presence or absence of cancer :in that organ or tissue.
For patients diagnosed with a gastrointestinal cancer, injection of an antibody which specifically binds CC2 can also have a therapeui~ic benefit. The antibody may exert its therapeutic effect alone. Alternatively, the antibody may be conjugated to a cytotoxic agent such as a drug, toxin or radionuclid<~ to enhance its therapeutic effect.
Drug monoclonal antibodies have been described in the art for example by Garnel~t and Baldwin, Cancer Research 1_986 46:2407-2412. The use of toxins conjugated to monoclonal antibodies for the therapy of various cancers has also been described by Pastan ~=_t al. Cell 1986 47:641-648. Yttrium-90 labeled monoclonal antibodies have been described for maximization of dose delivered to the tumor while limiting toxicity to normal tissues (Goodwin and Meares Cancer Supplement 1997 80:2675-2f80). Other cytotoxic radionuclides including, but not limited to Copper-67, Iodine-131 and Rhenium-186 can also be used for labeling of antibodies against CC2.
Antibodies which. can be used in these in vivo methods include polyclonal, monoclonal and omniclonal antibodies and antibodies prepared via molecular biology techniques.
Antibody fragments and aptamers and single-stranded oligonucleotides such as those derived from an in vitro evolution protocol referred to as SELEX and well known to those skilled in the art can also be used.
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 aspects of the invention, do not portray the limitations or circumscribe the scope of the disclosed invention.
EXAMPLES
The examples were 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) .
Real-Time quantitative PCR with fluorescent Taqman probes is a quantitat:ion 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, CA, USA).
Amplification of an endogenous control was 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) was used as this endogenous control. Tc> calculate relative quantitation between all the samples studied, the target RNA levels for one sample were used as the basis for comparative results (calibrator). Quantitation relative to the calibrator is 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 CC2 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 CC2. The results were analyzed using the ABI PRISM 7700 Sequence Detector and are provided in the following table. The absolute numbers are relative. levels of expression of CC2 compared to the kidney (calibrator).
The absolute numbers depicted in Table 1 are relative levels of expression of CC2 in 12 normal different tissues.
All the values are compared to normal kidney (calibrator).
These RNA samples are commercially available pools, originated by pooling samples of a particular tissue from different individual;.
- 1$ -Table 1: Relative Levels of CC2 Expression in Pooled Samples Tissue _ NORMAL
Colon-Asce~_nding 536 Endometrium 0 Kidney 1 Liver 10 Ovary 4 Pancreas 22 Prostate 332 Small Intestine 2539 Spleen 0.0 Stomach 2062 Testis 112 Uterus 2 The relative levels of expression in Table 1 show that the higher level of expression of CC2 mRNA is in tissues from the gastrointestinal tract, small intestine (2539), stomach (2062), and colon (536), with a lower level of expression in prostate (332), and testis (112). These results establish that CC2 mRNA expression is highly specific for gastrointestinal tissues including not only the colon but also the small intestine and stomach.
The absolute numbers in Table 1 were obtained analyzing pools of samples of a particular tissue from different individuals. They should not be compared to the absolute numbers originated from RNA obtained from tissue samples of single individuals depicted in Table 2.
The absolute numbers depicted in Table 2 are relative levels of expression of CC2 in 78 pairs of matching samples. All the values are compared to normal kidney (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.
_ 19 -Table 2: Relative Levels of CC2 Expression in Pooled Samples Sample ID Tissue Cancer Normal Tissue Adjacent Tissue StoAC93 Stomach 1 64860 279026 Sto728 Stomach 2 0 40 Sto758S Stomach 3 21029 2903 Sto915S Stomach 4 3488 56 StoAC99 Stomach 5 1162 330 Sto115S Stomach 6 409 146 Stol5S Stomach 7 4636 14 Stol7S Stomach 8 59662 538 Sto261S Stomach 9 53061 8977 Sto264S Stomach 10 27992 84643 Sto27S Stomach 11 20784 61 Sto288S Stomach 12 0 67 Sto531S Stomach 13 53192 8847 Sto539S Stomach 14 1492 27 Sto542S Stomach 15 26382 425 Sto610S Stomach 16 1029 20 Sto88S Stomach 17 3846 12 StoAc44 Stomach 18 1.7 78 _ StoMT54 Stomach 19 971 67 StoTA73 Stomach 20 35653 6020 SmI2IXA Small :Cntestine 1 31016 10022 SmIH89 Small :Cntestine 2 645 2227 C1nB56 Colon-Cecum 1 6816 971 ClnAS95 Colon-Ascending 2 8757 5501 ClnCM67 Colon-Cecum 3 2394 578 ClnAS67 Colon-Ascending 4 1566 1198 WO 00/20640 PC'f/US99/22725 ClnAS43 Colon-Ascending 5 127934 923 ClnAS96 Colon-Ascending 6 96620 3316 ClnAS98 Colon Ascending 7 83822 392 ClnAS89 Colon-Ascending 8 10231 4 ClnTX01 Colon-Transverse 9 92 331 ClnTX89 Colon-Transverse 10 11119 17 ClnTX67 Colon-Transverse 11 683 189 ClnMT38 Colon-Splenic 0 6230 flexture 12 ClnSG89 Colon-Sigmoid 13 2557 1293 ClnSG67 Colon-Sigmoid 14 39 132 ClnSG33 Colon-Sigmoid 15 17080 118542 ClnSG45 Colon-Sigmoid 16 243 80 C1nB34 Colon-Rectosigmoid 17 130 11 CInCXGA Colon-Rectum 18 790 47152 ClnRC67 Colon-Rectum 19 724 419 ClnC9XR Colon-Rectosigmoid 20 425 113 ClnRS45 Colon-Rectosigmoid 21 42202 1:117 ClnRC01 Colon-Rectum 22 2693 99 ClnRC89 Colon-Rectum 23 0 2402 B1d46XK Bladder 1 0 0 B1d66X Bladder 2 15 4 B1d32XK Bladder 3 8.5 0.9 Kid126XD Kidney 1 5 5 Kidl2XD Kidney 2 2 0 KidSXD Kidney 3 3.7 0.8 Kid6XD Kidney 4 4.3 0 Kid106XD Kidney 5 0 0.8 Liv42X Liver 1 2 1 Livl5XA Liver 2 0.2 0.7 Liv99XA Liver 3 0 1..9 LngAC69 Lung 1 2 0 LngBR94 Lung 2 3 0 Lng47XQ Lung 3 0 0 Mam59X Mammary Gland 1 0 0 MamBOIIX Mammary Gland 2 0 0 MamA06X Mammary Gland 3 15 20 Ovr103X Ovary 1 4 0 Ovr130X Ovary ~, 3 3 Pan7lXL Pancrea~a 1 69458 15147 Pan82XP Pancreas 2 0 0 Pan77X Pancrea.~> 3 0 0 Pan92X Pancreas 4 9696 52 PanC044 Pancreas 5 34 0 Prol2B Prostate 1 21 2 Pro23B Prostate 2 23 6 Prol3XB Prostate 3 6 23 Pro34B Prostate 4 152 75 Pro20XB Prostate 5 112 13 Pro65XB Prostate 6 60 683 Tst39X 'Testis 1. 2361 17 Endo10479 Endometrium 1 32 0 Utr85XU Uterus 1. 0 0 0= Negative In the analysis of matching samples, the higher levels of expression for CC2 are in stomach, small intestine, and colon. This pattern shows a high degree of specificity for gastrointestinal tissues including, not only the colon, but also the stomach and small intestine. These results confirm the tissue specificity results obtained with the panel of normal pooled samples (shown in Table 1).
The level of mRNA expression in cancer samples and the isogenic normal adjacent tissue from the same individual were also compared. This comparison provides an indication of specificity for the cancer stage (e. g. different levels of mRNA expression in the cancer sample compared to the normal adjacent tissue). Table 2 shows overexpression of CC2 in T5 primary stomach cancer tissues compared with their respective normal adjacent (stomach samples #3, 9, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 19, and 20) . There is overexpression in th~~ cancer tissues for 75~ of the stomach matching samples tested (total of 20 stomach matching samples).
CC2 is also differentially expressed in the two tested matching samples for cancer of the small intestine. Sample #1 shows upregulation for the mRNA of CC2 in cancer, whereas sample #2, shows lower expression in cancer.
CC2 is differentially expressed in twenty-three matching samples for colon cancer. Samples #1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 13, 16, 17, 19, 20, 21 and 22 show upregulation for the mRNA of CC2 in cancer, whereas samples #9, 12, 14, 15, 18, and 23 show lower expression in the cancer sample when compared to the normal adjacent tissue.
Altogether, the high level of tissue specificity for gastrointestinal tisaues, plus the mRNA differential expression in several of the primary stomach, small intestine, and colon matching samples tested indicate CC2 to be a diagnostic marker for gastrointestinal cancers including not only colon cancer, but also stomach cancer and cancer of the small intestine.
SEQUENCE LISTING
<110> Macina, Roberto A.
DIADEXUS LLC
<120> A Novel Method of Diagnosing, Monitoring, Staging, Imaging and Treating Gastrointestinal Cancers <130> DEX-0047 <140>
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FIELD OF THE INVENTION
This invention relates, in part, to newly developed assays for detecting, diagnosing, monitoring, staging prognosticating, imaging and treating cancers, particularly gastrointestinal cancers including cancer of the stomach, small intestine and colon.
BACKGROUND OF THE INVENTION
Cancer of the colon is the second most frequently diagnosed malignancy in the United States, as well as the second most common cause of cancer death. Colon cancer is a highly treatable and often curable disease when localized to the bowel. Surgery is the primary treatment and results in cure in approximately 50°s of patients. However, recurrence and metastases following surgery is a major problem and often is the ultimate cause of death.
Due to its proximity, cancer of the colon often metastasizes to the small intestine. The prognosis of the cancer spreading to the small intestine is 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 colon cancer. Various characteristics also assist in prognosticating colon cancer arid its spread to the small intestines. For example, bowel obstruction and bowel perforation are indicators of poor prognosis.
Elevated pretreatment serum levels of carcinoembryonic antigen (CEA) and of carbohydrate antigen 19-9 (CA 19-9) also have a negative prognostic significance. However, age greater than 70 years at presentation is not a contraindication to standard therapies; acceptable morbidity and mortality, as well as long-term survival, are achieved in this patient population.
Cancer cells can also originate in the small intestine. However, this :is a much rarer type of cancer.
Symptoms of cancer of the small intestine typically include pain or cramps in the middle of the abdomen, weight loss without dieting, a lump in the abdomen or blood in the stool.
Cancer of the stomach, also referred to as gastric cancer, also frequently metastasizes to the small intestine due to its proximity. This cancer is often difficult to diagnose in early stages and can be in the stomach for a long time, growing to a large size before symptoms arise.
In the early stages of cancer of the stomach, an individual may experience indigestion and stomach discomfort, a bloated feeling after' eating, mild nausea, loss of appetite or heartburn. In more advanced stages of stomach cancer, there may be blood in. the stool, vomiting, weight loss or more severe pain.
Because of the frequency of these types of cancer (approximately 160,000 new cases of colon and rectal cancer per year alone), the identification of high-risk groups, the demonstrated slow growth of primary lesions and the better survival of early-stage lesions, screening for gastrointestinal cancers 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 cancer of the colon, small intestine or stomach are of critical importance to the outcome of the patient. Patients diagnosed with early stage cancer generally have a much greater five-year survival rate as compared to the survival rate for patients diagnosed with distant metastasized cancers. New diagnostic methods which are more sensitive and specific for detecting early cancer of the stomach, small intestine and colon are clearly needed.
Patients with gastrointestinal cancers are closely monitored following initial therapy and during adjuvant therapy to determine response t:o therapy and to detect persistent or recurrent disease of metastasis. There is clearly a need for a cancer' marker which is more sensitive and specific in detecting recurrence of these types of cancer.
Another important step in managing gastrointestinal cancers is to determine the stage of the patient's disease.
Stage determination has potential prognostic value and provides criteria for designing optimal therapy.
Generally, pathological staging of cancer is preferable over clinical staging because the former gives a more accurate prognosis. However, clinical staging would be preferred were it at least as accurate as pathological staging because it does not depend on an invasive procedure to obtain tissue for pathological evaluation. Staging of gastrointestinal cancers would be improved by identifying new markers in cells, tissues, or bodily fluids which could differentiate between different stages of invasion.
Thirteen colon specific genes and naturally occurring variants thereof, referred to as CSGl-13, are disclosed in U.S. Patent 5,733,748 and WO 96/39541 for use as diagnostic markers in colon cancer. Some of these genes and polypeptides encoded thereby are also taught to be useful in determining if the colon cancer has metastasized.
U.S. Patent 5,,861,494, which issued January 19, 1999, also discloses a gene and polypeptide encoded thereby for use as a diagnostic marker for colon cancer and as an agent for determining if t:he colon cancer has metastasized. This gene and the polypeptide encoded thereby are similar in sequence to the cancer specific gene referred to herein as CC2.
It has now been found that CC2 is a useful diagnostic and metastatic marker not only for colon cancer but also for cancer of the stomach and small intestine. Thus, in the present invention,,, methods are provided for detecting, diagnosing, monitoring, staging, prognosticating, imaging and treating gastrointestinal cancers including cancer of the stomach, small intestine and colon via the cancer specific gene referred to herein as CC2. CC2 refers, among other things, to native protein expressed by the gene comprising the polynuc:leotide sequence of SEQ ID N0:1. The amino acid sequence oi: a polypeptide encoded by SEQ ID NO:1 is depicted herein as SEQ ID N0:2. In the alternative, what is meant by CC2 as used herein, means the native mRNA
encoded by the gene comprising the polynucleotide sequence of SEQ ID NO:1 or levels of the gene comprising the polynucleotide sequence of SEQ ID N0:1.
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.
SUi~IARY 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 a gastrointestinal cancer by analyzing for changes in levels of CC2 in cells, tissues or bodily fluids compared with levels. of CC2 in preferably the same cells, tissues, or bodily fluid type of a normal human control, wherein a change in levels of CC2 in the patient versus the normal human control is associated with a gastrointestinal cancer.
Further provided is a method of diagnosing metastatic cancer in a patient having a gastrointestinal cancer which is not known to have metastasized by identifying a human patient suspected of having a gastrointestinal cancer that has metastasized; analyzing a sample of cells, tissues, or bodily fluid from such patient for CC2; comparing the CC2 levels in such cells, tissues, or bodily fluid with levels of CC2 in preferably the same cells, tissues, or bodily fluid type of a normal human control, wherein an increase in CC2 levels in the patient versus the normal human control is associated with a gastrointestinal cancer which has metastasized.
Also provided by the invention is a method of staging a gastrointestinal cancer in a human which has such cancer by identifying a human patient having such cancer;
analyzing a sample of_ cells, tissues, or bodily fluid from such patient for CC2; comparing CC2 levels in such cells, tissues, or bodily f)._uid with levels of CC2 in preferably the same cells, tis:>ues, or bodily fluid type of a normal human control sample, wherein an increase in CC2 levels in the patient versus the normal human control is associated with a cancer which is progressing and a decrease in the levels of CC2 is as:>ociated with a cancer which is regressing or in remission.
Further provided is a method of monitoring a gastrointestinal 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 CC2;
comparing the CC2 levels in such cells, tissue, or bodily fluid with levels o:E CC2 in preferably the same cells, tissues, or bodily fluid type of a normal human control sample, wherein an increase in CC2 levels in the patient versus the normal human control is associated with a cancer which has metastasized.
Further provided is a method of monitoring the change in stage of a gastrointestinal cancer in a human having such cancer by looking at levels of CC2 in a human having such cancer. The method comprises identifying a human patient having such cancer; periodically analyzing a sample of cells, tissues, o:r bodily fluid from such patient for CC2; comparing the CC2 levels in such cells, tissue, or bodily fluid with levels of CC2 in preferably the same cells, tissues, or bodily fluid type of a normal human control sample, wherein an increase in CC2 levels in the patient versus the normal human control is associated with a cancer which is progressing and a decrease in the levels of CC2 is associated with a cancer which is regressing or in remission.
Further provided are antibodies targeted against CC2 or fragments of such antibodies which can be used to detect or image localization of CC2 in a patient for the purpose of detecting or diagnosing a disease or condition. Such antibodies can be polyclonal, monoclonal, or omniclonal or prepared by molecular biology techniques. The term "antibody", as used herein and throughout the instant specification is also meant to include aptamers and single-stranded oligonucleotides such as those derived from an in vitro evolution protocol referred to as SELEX and well known to those skilled in the art. Antibodies can be labeled with a variety of detectable labels including, but not limited to, radioisotopes and paramagnetic metals.
These antibodies or_ f:ragments thereof can also be used as therapeutic agents in the treatment of diseases characterized by expression of CC2. In therapeutic applications, the antibody can be used without or with derivatization to a cytotoxic agent such as a radioisotope, enzyme, toxin, drug or a prodrug.
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, ar~a 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.
DETAILED 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 CC2 with those of CC2 in a normal human control. What is meant by levels of CC2 as used herein, means levels of the native protein expressed by the gene comprising the pol.ynucleotide sequence of SEQ ID N0:1.
The amino acid sequence of a polypeptide encoded by SEQ ID
NO:l is depicted herein as SEQ ID N0:2. In the alternative, what is meant by levels of CC2 as used herein, means levels of the 'native mRNA encoded by the gene comprising the polynucleotide sequence of SEQ ID N0:1 or levels of the gene comprising t:he polynucleotide sequence of SEQ ID NO:l. 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 overexpression of CC2 protein compared to normal control bodily fluids, cells, or tissue samples may be used to diagnose the presence of cancers, _ g _ and in particular gastrointestinal cancers. By gastrointestinal cancers it. is meant to include stomach cancer, cancer of the small intestine, and colon cancer.
All the methods of: the present invention may optionally include measuring levels of other cancer markers as well as CC2. Other cancer markers, in addition to CC2, useful in the present invention will depend on the cancer being tested and are known to those of skill in the art.
Diagnostic Asssys The present inv~antion provides methods for diagnosing the presence of a gastrointestinal cancer by analyzing for changes in levels of CC2 in cells, tissues or bodily fluids compared with levels of CC2 in cells, tissues or bodily fluids of preferably the same type from a normal human control, wherein a clnange in levels of CC2 in the patient versus the normal human control is associated with the presence of a gastrointestinal cancer.
Without limiting the instant invention, typically, for a quantitative diagnostic assay a positive result indicating the patient being tested has cancer is one in which cells, tissues or bodily fluid levels of the cancer marker, such as CC2, 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 the onset of metastatic gastrointestinal cancers in a patient having a gastrointestinal cancer which has not yet metastasized. In the method of the present invention, a human cancer patient suspected of having a gastrointestinal 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.
_ g _ In the present. invention, determining the presence of CC2 levels in cells, tissues or bodily fluid, is particularly useful for discriminating between gastrointestinal cancers which have not metastasized and gastrointestinal cancers which have metastasized. Existing techniques have difficulty discriminating between gastrointestinal cancers which have metastasized and gastrointestinal cancers which have not metastasized.
However, proper treatment selection is often dependent upon such knowledge.
In the present invention, the cancer marker level measured in cells, tissues or bodily fluid of a human patient is CC2. The measured CC2 level in the human patient is compared 'with levels of CC2_ in preferably the same cells, tissue or bodily fluid type of a normal human control. That is, if the cancer marker being observed is CC2 in serum, this level is preferably compared with the level of CC2 in serum of a normal human control. An increase in the CC2 in the patient versus the normal human control is associated with a gastrointestinal cancer which has metastasized.
Without l.imiti.ng the instant invention, typically, for a quantitative diagnostic assay a positive result indicating the cancer i.n the patient being tested or monitored has metastasized is one in which cells, tissues or bodily fluid levels of the cancer marker, such as CC2, are at least two times higher, and most preferably are at least five times higher, than i.n 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 preferably also include samples from a human patient that is determined by reliable methods to have a gastrointestinal cancer which has not metastasized.
Staging The invention also provides a method of staging gastrointestinal cancers in a human patient. The method comprises identifying a human patient having such cancer and analyzing a samplfs of cells, tissues or bodily fluid from such human patient for CC2. In this method CC2 levels in such cells, tissues or bodily fluid are then compared with levels of CC2 in preferably the same cells, tissues or bodily fluid type of a normal human control sample, wherein an increase in CC2 levels in the human patient versus the normal human control _is associated with a cancer which is progressing and a decrease in the levels of CC2 is associated with a cancer which is regressing or in remission.
Monitoring Further provided is a method of monitoring gastrointestinal cancers 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 human. patient for CC2; comparing the CC2 levels in such cells, tissues or bodily fluid with levels of CC2 in preferably the same cells, tissues or bodily fluid type of a normal human control, wherein an :increase in CC2 levels in the human patient versus the normal human control is associated with a cancer which has metastasized.
Further provided by this invention is a method of monitoring the change in stage of gastrointestinal cancers in a human having suwh cancer. The method comprises identifying a human patient having such cancer;
periodically analyzing a sample of cells, tissues or bodily fluid from such human patient for CC2; and comparing the ' CC2 levels in such cells, tissues or bodily fluid with levels of CC2 in preferably the same cells, tissues or bodily fluid type of a normal human control, wherein an increase in CC2 levels in the human patient versus the normal human control is associated with a cancer which is progressing in stage and a decrease in the levels of CC2 is associated with a cancer which is regressing in stage or in remission.
Monitoring such patient for onset of metastasis is periodic and preferalaly 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 (:including protein levels), such as CC2 of the present invention, in a sample derived from a patient are well known to those of skill in the art. Such assay methods include, without limitation, radioimmunoassays, reverse transcriptase PCR (RT-PCR) assays, immunohistoclnemistry assays, in situ hybridization assays, competitive-binding assays, Western Blot analyses, ELISA assays and proteomic approaches: two-dimensional gel electrophoresis (2D ~alectrophox~esis) and non-gel based approaches such as mass spectrometry or protein interaction profiling. 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 CC2, preferably a monoclonal antibody.
In addition a reporter antibody generally is prepared which binds specifically to CC2. 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 CC2 is incubated on a solid support, e.g. a polystyrene dish, that binds the antibody. Any free protein binding sites an 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 tame CC2 binds to the specific antibody attached to the polystyrene dish. Unbound sample is washed out with buffer. A reporter antibody specifically directed to CC2 and linked to horseradish peroxidase is placed in the dish resulting in binding of the reporter antibody to any monoclonal antibody bound to CC2. Unattached reporter antibody is then washed out. Reagents for peroxidase activity, including a coiorimetric substrate are then added to the dish.
Immobilized peroxidase, linked to CC2 antibodies, produces a colored reaction product. The amount of color developed in a given time period is proportional to the amount of_ CC2 protein present in the sample. Quantitative results typically are obtained by reference to a standard curve.
A competition assay can also be employed wherein antibodies specific 'to CC2 are attached to a solid support and labeled CC2 and a sample derived from the host are passed over the solid support. The amount of label detected which is attached to the solid support can be correlated to a quantity of CC2 in the sample.
Nucleic acid methods can also be used to detect CC2 mRNA as a marker for gastrointestinal cancers. 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 thausands of other mRNA species. In RT-PC:R, 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 detect both the expression of and quantitate the level of expression of a gene. In this approach, a cDNA encoding the CC2 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 CC2 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 irucluding 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.
Of the proteornic approaches, 2D electrophoresis is a technique well known to those in the art. Isolation of individual proteins from a sample such as serum is accomplished using sequential separation of proteins by different characteristics usually on polyacrylamide gels.
First, proteins are separated by size using an electric current. The current acts uniformly on all proteins, so smaller proteins move farther on the gel than larger proteins. The second dimension applies a current perpendicular to the first and separates proteins not on the basis of size but an the specific electric charge carried by each protein. Since no two proteins with different sequences are identical on the basis of both size and charge, the result of a 2D separation is a square gel in which each protein accupies a unique spot. Analysis of the spots with chemical or antibody probes, or subsequent protein microsequencing can reveal the relative abundance of a given protein a:nd the identity of the proteins in the sample.
The above tests can be carried out on samples derived from a variety of cells, bodily fluids and/or tissue extracts (homogenates or solubilized tissue) obtained from a patient including 'those from tissue biopsies 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.
In Vivo Antibody Use Antibodies which specifically bind to CC2 can also be used in vivo in patients suspected of suffering from gastrointestinal cancers including stomach cancer, cancer of the small intestine, and colon cancer. Specifically, antibodies which specifically bind a CC2 can be injected into a patient suspected of having a gastrointestinal cancer for diagnostic and/or therapeutic purposes. The preparation and use of antibodies for in vivo diagnosis is well known in the art. For example, antibody-chelators labeled with Indium-111 have been described for use in the radioimmunoscintographi.c imaging of carcinoembryonic antigen expressing tumors (Sumerdon et al. Nucl. Med. Biol.
1990 17:247-254). I:n particular, these antibody-chelators have been used in detecting tumors in patients suspected of having recurrent colorectal cancer (Griffin et al. J. Clin.
Onc. 1991 9:631-640).. Antibodies with paramagnetic ions as labels for use in magnetic resonance imaging have also been described (Lauffer, R.B. Magnetic Resonance in Medicine 1991 22:339-342). Antibodies directed against CC2 can be used in a similar manner. Labeled antibodies which specifically bind CCa? can be injected into patients suspected of having a gastrointestinal cancer for the purpose of diagnosing or staging of the disease status of the patient. The label used will be selected in accordance with the imaging modality to be used. For example, radioactive labels such as Indium-111, Technetium-99m or Iodine-131 can be usE~d for planar scans or single photon emission computed tornography (SPELT). Positron emitting labels such as Fluor~~ne-19 can be used in positron emission tomography. Paramagnetic ions such as Gadlinium (III) or Manganese (II) can be' used in magnetic resonance imaging (MRI). Localization of the label permits determination of the spread of the cancer. The amount of label within an organ or tissue also allows determination of the presence or absence of cancer :in that organ or tissue.
For patients diagnosed with a gastrointestinal cancer, injection of an antibody which specifically binds CC2 can also have a therapeui~ic benefit. The antibody may exert its therapeutic effect alone. Alternatively, the antibody may be conjugated to a cytotoxic agent such as a drug, toxin or radionuclid<~ to enhance its therapeutic effect.
Drug monoclonal antibodies have been described in the art for example by Garnel~t and Baldwin, Cancer Research 1_986 46:2407-2412. The use of toxins conjugated to monoclonal antibodies for the therapy of various cancers has also been described by Pastan ~=_t al. Cell 1986 47:641-648. Yttrium-90 labeled monoclonal antibodies have been described for maximization of dose delivered to the tumor while limiting toxicity to normal tissues (Goodwin and Meares Cancer Supplement 1997 80:2675-2f80). Other cytotoxic radionuclides including, but not limited to Copper-67, Iodine-131 and Rhenium-186 can also be used for labeling of antibodies against CC2.
Antibodies which. can be used in these in vivo methods include polyclonal, monoclonal and omniclonal antibodies and antibodies prepared via molecular biology techniques.
Antibody fragments and aptamers and single-stranded oligonucleotides such as those derived from an in vitro evolution protocol referred to as SELEX and well known to those skilled in the art can also be used.
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 aspects of the invention, do not portray the limitations or circumscribe the scope of the disclosed invention.
EXAMPLES
The examples were 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) .
Real-Time quantitative PCR with fluorescent Taqman probes is a quantitat:ion 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, CA, USA).
Amplification of an endogenous control was 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) was used as this endogenous control. Tc> calculate relative quantitation between all the samples studied, the target RNA levels for one sample were used as the basis for comparative results (calibrator). Quantitation relative to the calibrator is 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 CC2 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 CC2. The results were analyzed using the ABI PRISM 7700 Sequence Detector and are provided in the following table. The absolute numbers are relative. levels of expression of CC2 compared to the kidney (calibrator).
The absolute numbers depicted in Table 1 are relative levels of expression of CC2 in 12 normal different tissues.
All the values are compared to normal kidney (calibrator).
These RNA samples are commercially available pools, originated by pooling samples of a particular tissue from different individual;.
- 1$ -Table 1: Relative Levels of CC2 Expression in Pooled Samples Tissue _ NORMAL
Colon-Asce~_nding 536 Endometrium 0 Kidney 1 Liver 10 Ovary 4 Pancreas 22 Prostate 332 Small Intestine 2539 Spleen 0.0 Stomach 2062 Testis 112 Uterus 2 The relative levels of expression in Table 1 show that the higher level of expression of CC2 mRNA is in tissues from the gastrointestinal tract, small intestine (2539), stomach (2062), and colon (536), with a lower level of expression in prostate (332), and testis (112). These results establish that CC2 mRNA expression is highly specific for gastrointestinal tissues including not only the colon but also the small intestine and stomach.
The absolute numbers in Table 1 were obtained analyzing pools of samples of a particular tissue from different individuals. They should not be compared to the absolute numbers originated from RNA obtained from tissue samples of single individuals depicted in Table 2.
The absolute numbers depicted in Table 2 are relative levels of expression of CC2 in 78 pairs of matching samples. All the values are compared to normal kidney (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.
_ 19 -Table 2: Relative Levels of CC2 Expression in Pooled Samples Sample ID Tissue Cancer Normal Tissue Adjacent Tissue StoAC93 Stomach 1 64860 279026 Sto728 Stomach 2 0 40 Sto758S Stomach 3 21029 2903 Sto915S Stomach 4 3488 56 StoAC99 Stomach 5 1162 330 Sto115S Stomach 6 409 146 Stol5S Stomach 7 4636 14 Stol7S Stomach 8 59662 538 Sto261S Stomach 9 53061 8977 Sto264S Stomach 10 27992 84643 Sto27S Stomach 11 20784 61 Sto288S Stomach 12 0 67 Sto531S Stomach 13 53192 8847 Sto539S Stomach 14 1492 27 Sto542S Stomach 15 26382 425 Sto610S Stomach 16 1029 20 Sto88S Stomach 17 3846 12 StoAc44 Stomach 18 1.7 78 _ StoMT54 Stomach 19 971 67 StoTA73 Stomach 20 35653 6020 SmI2IXA Small :Cntestine 1 31016 10022 SmIH89 Small :Cntestine 2 645 2227 C1nB56 Colon-Cecum 1 6816 971 ClnAS95 Colon-Ascending 2 8757 5501 ClnCM67 Colon-Cecum 3 2394 578 ClnAS67 Colon-Ascending 4 1566 1198 WO 00/20640 PC'f/US99/22725 ClnAS43 Colon-Ascending 5 127934 923 ClnAS96 Colon-Ascending 6 96620 3316 ClnAS98 Colon Ascending 7 83822 392 ClnAS89 Colon-Ascending 8 10231 4 ClnTX01 Colon-Transverse 9 92 331 ClnTX89 Colon-Transverse 10 11119 17 ClnTX67 Colon-Transverse 11 683 189 ClnMT38 Colon-Splenic 0 6230 flexture 12 ClnSG89 Colon-Sigmoid 13 2557 1293 ClnSG67 Colon-Sigmoid 14 39 132 ClnSG33 Colon-Sigmoid 15 17080 118542 ClnSG45 Colon-Sigmoid 16 243 80 C1nB34 Colon-Rectosigmoid 17 130 11 CInCXGA Colon-Rectum 18 790 47152 ClnRC67 Colon-Rectum 19 724 419 ClnC9XR Colon-Rectosigmoid 20 425 113 ClnRS45 Colon-Rectosigmoid 21 42202 1:117 ClnRC01 Colon-Rectum 22 2693 99 ClnRC89 Colon-Rectum 23 0 2402 B1d46XK Bladder 1 0 0 B1d66X Bladder 2 15 4 B1d32XK Bladder 3 8.5 0.9 Kid126XD Kidney 1 5 5 Kidl2XD Kidney 2 2 0 KidSXD Kidney 3 3.7 0.8 Kid6XD Kidney 4 4.3 0 Kid106XD Kidney 5 0 0.8 Liv42X Liver 1 2 1 Livl5XA Liver 2 0.2 0.7 Liv99XA Liver 3 0 1..9 LngAC69 Lung 1 2 0 LngBR94 Lung 2 3 0 Lng47XQ Lung 3 0 0 Mam59X Mammary Gland 1 0 0 MamBOIIX Mammary Gland 2 0 0 MamA06X Mammary Gland 3 15 20 Ovr103X Ovary 1 4 0 Ovr130X Ovary ~, 3 3 Pan7lXL Pancrea~a 1 69458 15147 Pan82XP Pancreas 2 0 0 Pan77X Pancrea.~> 3 0 0 Pan92X Pancreas 4 9696 52 PanC044 Pancreas 5 34 0 Prol2B Prostate 1 21 2 Pro23B Prostate 2 23 6 Prol3XB Prostate 3 6 23 Pro34B Prostate 4 152 75 Pro20XB Prostate 5 112 13 Pro65XB Prostate 6 60 683 Tst39X 'Testis 1. 2361 17 Endo10479 Endometrium 1 32 0 Utr85XU Uterus 1. 0 0 0= Negative In the analysis of matching samples, the higher levels of expression for CC2 are in stomach, small intestine, and colon. This pattern shows a high degree of specificity for gastrointestinal tissues including, not only the colon, but also the stomach and small intestine. These results confirm the tissue specificity results obtained with the panel of normal pooled samples (shown in Table 1).
The level of mRNA expression in cancer samples and the isogenic normal adjacent tissue from the same individual were also compared. This comparison provides an indication of specificity for the cancer stage (e. g. different levels of mRNA expression in the cancer sample compared to the normal adjacent tissue). Table 2 shows overexpression of CC2 in T5 primary stomach cancer tissues compared with their respective normal adjacent (stomach samples #3, 9, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 19, and 20) . There is overexpression in th~~ cancer tissues for 75~ of the stomach matching samples tested (total of 20 stomach matching samples).
CC2 is also differentially expressed in the two tested matching samples for cancer of the small intestine. Sample #1 shows upregulation for the mRNA of CC2 in cancer, whereas sample #2, shows lower expression in cancer.
CC2 is differentially expressed in twenty-three matching samples for colon cancer. Samples #1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 13, 16, 17, 19, 20, 21 and 22 show upregulation for the mRNA of CC2 in cancer, whereas samples #9, 12, 14, 15, 18, and 23 show lower expression in the cancer sample when compared to the normal adjacent tissue.
Altogether, the high level of tissue specificity for gastrointestinal tisaues, plus the mRNA differential expression in several of the primary stomach, small intestine, and colon matching samples tested indicate CC2 to be a diagnostic marker for gastrointestinal cancers including not only colon cancer, but also stomach cancer and cancer of the small intestine.
SEQUENCE LISTING
<110> Macina, Roberto A.
DIADEXUS LLC
<120> A Novel Method of Diagnosing, Monitoring, Staging, Imaging and Treating Gastrointestinal Cancers <130> DEX-0047 <140>
<141>
<150> 60/102,879 <151> 1998-10-02 <160> 2 <170> PatentIn Ver. 2.0 <210> 1 <211> 1255 <212> DNA
<213> Homo sapiens <220>
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Claims (11)
1. A method for diagnosing the presence of a gastrointestinal cancer in a patient comprising:
(a) measuring levels of CC2 in cells, tissues or bodily fluids in a patient; and (b) comparing the measured levels of CC2 with levels of CC2 in cells, tissues or bodily fluids from a normal human control, wherein a change in.measured levels of CC2 in said patient versus normal human control is associated with the presence of a gastrointestinal cancer.
(a) measuring levels of CC2 in cells, tissues or bodily fluids in a patient; and (b) comparing the measured levels of CC2 with levels of CC2 in cells, tissues or bodily fluids from a normal human control, wherein a change in.measured levels of CC2 in said patient versus normal human control is associated with the presence of a gastrointestinal cancer.
2. A method of diagnosing metastases of a gastrointestinal cancer in a patient comprising:
(a) identifying a patient having a gastrointestinal cancer that is not known to have metastasized;
(b) measuring CC2 levels in a sample of cells, tissues, or bodily fluid from said patient; and (c) comparing the measured CC2 levels with levels of CC2 in cells, tissue, or bodily fluid of a normal human control, wherein an increase in measured CC2 levels in the patient versus the normal human control is associated with a cancer which has metastasized.
(a) identifying a patient having a gastrointestinal cancer that is not known to have metastasized;
(b) measuring CC2 levels in a sample of cells, tissues, or bodily fluid from said patient; and (c) comparing the measured CC2 levels with levels of CC2 in cells, tissue, or bodily fluid of a normal human control, wherein an increase in measured CC2 levels in the patient versus the normal human control is associated with a cancer which has metastasized.
3. A method of staging a gastrointestinal cancer in a patient having a gastrointestinal cancer comprising:
(a) identifying a patient having a gastrointestinal cancer;
(b) measuring CC2 levels in a sample of cells, tissue, or bodily fluid from said patient; and (c) comparing measured CC2 levels with levels of CC2 in cells, tissues, or bodily fluid of a normal human control, wherein an increase in measured CC2 levels in said patient versus the normal human control is associated with a cancer which is progressing and a decrease in the measured CC2 levels is associated with a cancer which is regressing or in remission.
(a) identifying a patient having a gastrointestinal cancer;
(b) measuring CC2 levels in a sample of cells, tissue, or bodily fluid from said patient; and (c) comparing measured CC2 levels with levels of CC2 in cells, tissues, or bodily fluid of a normal human control, wherein an increase in measured CC2 levels in said patient versus the normal human control is associated with a cancer which is progressing and a decrease in the measured CC2 levels is associated with a cancer which is regressing or in remission.
4. A method of monitoring a gastrointestinal cancer in a patient for the onset of metastasis comprising:
(a) identifying a patient having a gastrointestinal cancer that is not known to have metastasized;
(b) periodically measuring levels of CC2 in samples of cells, tissues, or bodily fluid from said patient; and (c) comparing the periodically measured CC2 levels with levels of CC2 in cells, tissues, or bodily fluid of a normal human control, wherein an increase in any one of the periodically measured CC2 levels in the patient versus the normal human control is associated with a cancer which has metastasized.
(a) identifying a patient having a gastrointestinal cancer that is not known to have metastasized;
(b) periodically measuring levels of CC2 in samples of cells, tissues, or bodily fluid from said patient; and (c) comparing the periodically measured CC2 levels with levels of CC2 in cells, tissues, or bodily fluid of a normal human control, wherein an increase in any one of the periodically measured CC2 levels in the patient versus the normal human control is associated with a cancer which has metastasized.
5. A method of monitoring a change in stage of a gastrointestinal cancer in a patient comprising:
(a) identifying a patient having a gastrointestinal cancer;
(b) periodically measuring levels of CC2 in cells, tissues, or bodily fluid from said patient; and (c) comparing the periodically measured CC2 levels with levels of CC2 in cells, tissues, or bodily fluid of a normal human control, wherein an increase in any one of the periodically measured CC2 levels in the patient versus the normal human control is associated with a cancer which is progressing in stage and a decrease is associated with a cancer which is regressing in stage or in remission.
(a) identifying a patient having a gastrointestinal cancer;
(b) periodically measuring levels of CC2 in cells, tissues, or bodily fluid from said patient; and (c) comparing the periodically measured CC2 levels with levels of CC2 in cells, tissues, or bodily fluid of a normal human control, wherein an increase in any one of the periodically measured CC2 levels in the patient versus the normal human control is associated with a cancer which is progressing in stage and a decrease is associated with a cancer which is regressing in stage or in remission.
6. The method of claim 1, 2, 3, 4 or 5 wherein the CC2 comprises SEQ ID NO:1 or SEQ ID N0:2.
7. An antibody which specifically binds CC2.
8. A method of imaging a gastrointestinal cancer in a patient comprising administering to the patient an antibody of claim 7.
9. The method of claim 8 wherein said antibody is labeled with paramagnetic ions or a radioisotope.
10. A method of treating a gastrointestinal cancer in a patient comprising administering to the patient an antibody of claim 7.
11. The method of claim 10 wherein the antibody is conjugated to a cytotoxic agent.
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US10287998P | 1998-10-02 | 1998-10-02 | |
| US60/102,879 | 1998-10-02 | ||
| PCT/US1999/022725 WO2000020640A1 (en) | 1998-10-02 | 1999-09-30 | A novel method of diagnosing, monitoring, staging, imaging and treating gastrointestinal cancers |
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| CA2345000A1 true CA2345000A1 (en) | 2000-04-13 |
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| CA002345000A Abandoned CA2345000A1 (en) | 1998-10-02 | 1999-09-30 | A novel method of diagnosing, monitoring, staging, imaging and treating gastrointestinal cancers |
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| EP (1) | EP1117833A4 (en) |
| JP (1) | JP2002526760A (en) |
| CA (1) | CA2345000A1 (en) |
| WO (1) | WO2000020640A1 (en) |
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| US6962779B1 (en) | 1998-10-02 | 2005-11-08 | Diadexus, Inc. | Method of diagnosing, monitoring, staging, imaging and treating gastrointestinal cancers |
| CA2404431C (en) | 2000-03-27 | 2011-06-07 | Thomas Jefferson University | Guanylyl cyclase c in the detection of stomach and esophageal cancers |
| US6774223B2 (en) * | 2000-06-28 | 2004-08-10 | Diadexus, Inc. | Method of diagnosing, monitoring, staging, imaging and treating colon cancer |
| AU784548B2 (en) * | 2001-03-16 | 2006-04-27 | Ortho-Clinical Diagnostics, Inc. | Reg-like protein |
| US7560531B2 (en) | 2003-05-29 | 2009-07-14 | Diadexus, Inc. | Cln101 antibody compositions and methods of use alone and in combination with prostate specific antigen and other cancer markers |
| US20060134653A1 (en) * | 2004-07-28 | 2006-06-22 | Bayer Healthcare Llc | Differential expression of genes in microsatellite instability |
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| US5861494A (en) * | 1995-06-06 | 1999-01-19 | Human Genome Sciences, Inc. | Colon specific gene and protein |
| WO1996039541A1 (en) * | 1995-06-06 | 1996-12-12 | Human Genome Sciences, Inc. | Colon specific gene and protein |
| AU4220797A (en) * | 1996-09-13 | 1998-04-02 | Protegene Inc. | Human proteins having secretory signal sequences and DNAs encoding these prot eins |
| US5837841A (en) * | 1996-10-11 | 1998-11-17 | Incyte Pharmaceuticals, Inc. | Human Reg protein |
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- 1999-09-30 EP EP99950047A patent/EP1117833A4/en not_active Withdrawn
- 1999-09-30 JP JP2000574732A patent/JP2002526760A/en not_active Withdrawn
- 1999-09-30 WO PCT/US1999/022725 patent/WO2000020640A1/en not_active Application Discontinuation
- 1999-09-30 CA CA002345000A patent/CA2345000A1/en not_active Abandoned
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| EP1117833A1 (en) | 2001-07-25 |
| JP2002526760A (en) | 2002-08-20 |
| EP1117833A4 (en) | 2002-08-14 |
| WO2000020640A1 (en) | 2000-04-13 |
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