Method for predicting and detecting tumor metastasis

Abstract

The invention provides a method of determining the prognosis of cancer in a subject. The method comprises (a) obtaining a sample from the subject, (b) analyzing the sample for the expression level of a carboxypeptidase E (CPE) splice variant, and (c) correlating the expression level in the sample with the prognosis of cancer in the subject. The invention further provides a method of diagnosing cancer, methods of treatment, kits for detecting mRNA expression of a CPE-ΔN, and inhibitors of CPE-ΔN and compositions thereof.

1 . A method of determining the prognosis of cancer in a subject, the method comprising
 (a) obtaining a sample from the subject,   (b) analyzing the sample for an expression level of a carboxypeptidase E (CPE) splice variant that lacks the N terminus (CPE-ΔN), and   (c) correlating the expression level of CPE-ΔN in the sample to the prognosis of cancer in the subject.   
     
     
         2 . The method of  claim 1 , wherein the prognosis is that the cancer is a metastatic lesion. 
     
     
         3 . The method of  claim 1 , wherein the prognosis is that the cancer is likely to metastasize. 
     
     
         4 . The method of  claim 1 , wherein the prognosis is that the cancer is not a metastatic lesion. 
     
     
         5 . The method of  claim 1 , wherein the prognosis is that the cancer is not likely to metastasize. 
     
     
         6 . The method of  claim 1 , further comprising determining a treatment course for the subject in accordance with the prognosis. 
     
     
         7 . A method of diagnosing cancer in a subject, the method comprising
 (a) obtaining a sample from the subject,   (b) analyzing the sample for an expression level of a carboxypeptidase E (CPE) splice variant that lacks the N terminus (CPE-ΔN), and   (c) correlating the expression level of CPE-ΔN in the sample to a diagnosis of cancer in the subject.   
     
     
         8 . The method of  claim 7 , wherein the diagnosis is that the subject has cancer. 
     
     
         9 . The method of  claim 8 , wherein the diagnosis is that the cancer is benign or malignant. 
     
     
         10 . The method of  claim 8 , wherein the diagnosis is that the cancer is metastatic. 
     
     
         11 . The method of  claim 7 , further comprising determining a treatment course for the subject in accordance with the diagnosis. 
     
     
         12 . The method of  claim 1 , wherein the sample is selected from the group consisting of tissue, blood, and a combination thereof. 
     
     
         13 . The method of  claim 12 , wherein the sample is tissue, and the tissue is selected from the group consisting of nerve, adrenal, thyroid, liver, lung, colorectal, breast, head and neck, skin, pancreatic, ovarian, cervical, paraganglioma, pheochromocytoma, melanoma, esophagus, cervical, brain, and stomach cancer. 
     
     
         14 . The method of  claim 13 , wherein the tissue is selected from the group consisting of tumor, tissue surrounding the tumor, and a combination thereof. 
     
     
         15 . The method of  claim 1 , wherein the expression level of CPE-ΔN is determined using copy number of CPE-ΔN mRNA. 
     
     
         16 . The method of  claim 15 , wherein the sample is a pheochromocytoma/paraganglioma (PHEO/PGL). 
     
     
         17 . The method of  claim 16 , wherein a copy number of CPE-ΔN mRNA of less than about 200,000 is correlated to a prognosis of the PHEO/PGL tumor as benign and of about 1 million or greater is correlated to a prognosis of the PHEO/PGL tumor as metastatic. 
     
     
         18 . The method of  claim 15 , wherein the sample is a differentiated thyroid carcinoma (DTC). 
     
     
         19 . The method of  claim 18 , wherein a copy number of CPE-ΔN mRNA of less than about 200,000 is correlated to a prognosis of the DTC tumor as benign, of between about 200,000 to about 600,000 is correlated to a prognosis of no metastasis of the DTC tumor, of about 600,000 to about 1 million is correlated to a prognosis of likely metastasis of the DTC tumor, and of about greater than 1 million is correlated to a prognosis of the DTC tumor as metastatic. 
     
     
         20 . A method of treating cancer in a subject, comprising administering an effective amount of an inhibitor of a carboxypeptidase E (CPE) splice variant that lacks the N terminus (CPE-ΔN) to a subject to treat a cancer in the subject. 
     
     
         21 . The method of  claim 20 , wherein the inhibitor comprises a nucleic acid complementary to a DNA or mRNA of CPE-ΔN. 
     
     
         22 . The method of  claim 20 , wherein the method further comprises administering a chemotherapeutic agent to the subject. 
     
     
         23 . The method of  claim 20 , wherein the cancer is selected from the group consisting of nerve, adrenal, thyroid, liver, lung, colorectal, breast, head and neck, skin, pancreatic, ovarian, cervical, paraganglioma, pheochromocytoma, melanoma, esophagus, cervical, brain, and stomach cancer. 
     
     
         24 . The method of  claim 1 , wherein CPE-ΔN polypeptide comprises SEQ ID NO: 2. 
     
     
         25 . The method of  claim 1 , wherein CPE-ΔN polypeptide is encoded by a nucleic acid comprising SEQ ID NO: 1. 
     
     
         26 . A composition comprising an inhibitor of a carboxypeptidase E (CPE) splice variant that lacks the N terminus (CPE-ΔN) and a pharmaceutically acceptable carrier. 
     
     
         27 . The composition of  claim 26 , wherein the inhibitor comprises a nucleic acid complementary to the DNA or mRNA of the CPE splice variant. 
     
     
         28 . The composition of  claim 27 , wherein the inhibitor is selected from the group consisting of siRNA, cDNA, and antisense. 
     
     
         29 . The composition of  claim 26 , wherein the inhibitor comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO: 25, SEQ ID NO: 26, and SEQ ID NO: 27. 
     
     
         30 . An isolated nucleic acid comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: 25, SEQ ID NO: 26, and SEQ ID NO: 27. 
     
     
         31 . A kit for detecting mRNA expression of a carboxypeptidase E (CPE) splice variant that lacks the N terminus (CPE-ΔN) or polypeptide levels of CPE-ΔN comprising one or more primers or probes that detect CPE-ΔN mRNA or CPE-ΔN polypeptide. 
     
     
         32 . The kit of  claim 31 , wherein the one or more primers do not amplify wild-type CPE mRNA. 
     
     
         33 . The kit of  claim 31 , wherein the one or more primers include SEQ ID NO: 5 and SEQ ID NO: 6. 
     
     
         34 . The kit of  claim 31 , wherein the one or more probes do not specifically bind wild-type CPE mRNA or wild-type CPE polypeptide. 
     
     
         35 . The kit of  claim 31 , wherein the one or more probes are antibodies. 
     
     
         36 . A method of detecting expression of a carboxypeptidase E (CPE) splice variant that lacks the N terminus (CPE-ΔN) or polypeptide levels of CPE-ΔN in a sample comprising
 (a) obtaining a sample from the subject, and 
 (b) contacting the sample with one or more primers or probes that detect CPE-ΔN mRNA or CPE-ΔN polypeptide, 
 thereby detecting expression of CPE-ΔN mRNA or CPE-ΔN polypeptide levels. 
 
     
     
         37 . The method of  claim 36 , wherein the one or more probes do not specifically bind wild-type CPE mRNA or wild-type CPE polypeptide. 
     
     
         38 . The method of  claim 36 , wherein the one or more probes are antibodies.