Diagnostic and Prognostic Markers for Cancer

Abstract

Compositions and methods useful for diagnosis and prognosis of cancer are provided.

1 . A method of predicting the risk of cancer recurrence in a patient, comprising:
 a) analyzing expression levels of at least two iron homeostasis-associated markers (IHA) set forth in Table II in a sample obtained from said patient;   b) comparing the expression levels of said at least two IHA markers in said sample to levels observed in patient cohorts exhibiting distant metastasis-free survival for at least five years, and assigning said patient to a risk group based on correlation with levels observed in previously analyzed patient cohorts of known outcome, thereby predicting said patients risk of cancer recurrence.   
     
     
         2 . The method of  claim 1 , wherein said cancer is breast, ovarian or prostate cancer and said at least two markers are ferroportin and hepcidin wherein high ferroportin levels in the presence of low hepcidin levels are indicative of a lowered risk of recurrent disease. 
     
     
         3 . The method of  claim 1 , wherein said cancer is breast cancer and said at least two markers are HFE and TFRC, wherein high HFE levels in the presence of low TFRC levels are indicative of a lowered risk of recurrent disease. 
     
     
         4 . The method of  claim 1 , wherein said cancer is breast cancer and said at least two markers are CYBRD1 and SCARA5, wherein reduced expression of said markers in said patient sample is indicative of an increased risk for recurrence. 
     
     
         5 . The method of  claim 1 , further comprising analyzing levels of additional iron homeostasis associated marker molecule(s) selected from the group consisting of FTL, IREB2 protein, TFRC, TF, TMPRSS6 and FTH1. 
     
     
         6 . The method of  claim 1 , wherein said cancer is breast cancer and expression levels of six IHA makers are analyzed, said markers being Ferroportin, CyBRD1, STEAP1, STEAP2, ISCU and TFRC, wherein high expression levels of Ferroportin, CYBRD1, STEAP1, STEAP2, ISCU in the presence of a low expression level for TFRC is associated with a decreased risk of recurrent disease. 
     
     
         7 . The method of  claim 1 , wherein said cancer is breast cancer and expression levels of the iron regulatory gene signature set forth in Table III or Table IV are determined. 
     
     
         8 . The method of  claims 1  to  7  wherein said analyzing step comprises contacting said sample with an agent having affinity for said IHA markers, said agent forming a specific binding pair with said at least two markers, said agent comprising a detectable label, measuring said detectable label, thereby determining expression level of said markers in said sample. 
     
     
         9 . The method of  claims 1  to  8  wherein said markers are selected from the group consisting of polypeptides, nucleic acids or informational sequence fragments thereof fragments thereof. 
     
     
         10 . The method as claimed in  claim 8 , wherein said IHA markers comprise polypeptides or fragments thereof, said agent is an antibody or fragment thereof and said polypeptide is detected by a method selected from the group consisting of flow cytometric analysis, immunohisto-chemical detection and immunoblot analysis. 
     
     
         11 . The method as claimed in  claim 8  wherein said molecules comprise nucleic acids or fragments thereof, said agent is complementary nucleic acids which hybridizes to said molecules and said iron homeostasis associated nucleic acid is detected by a method selected from the group consisting of in situ hybridization assay, hybridization assay, gel electrophoresis, RT-PCR, real time PCR, and microarray analysis. 
     
     
         12 . The method of  claim 1 , wherein said analyzing is genetic analysis performed on a computer using previously sequenced patient samples. 
     
     
         13 . The method as claimed in  claim 1 , wherein said biological sample is a biopsy. 
     
     
         14 . The method of  claim 1 , wherein said biological sample is selected from the group consisting of formalin fixed paraffin embedded tissue or cells, processed tissue, frozen tissue, blood cells, breast cancer cells, ovarian cancer cells, colon cancer cells, uterine cancer cells and prostate cancer cells. 
     
     
         15 . The method of  claim 1 , wherein said cancer is breast cancer optionally comprising the step of determining at least one parameter selected from the group consisting of estrogen receptor (ER) status, her2-neu status, progesterone receptor status, histological grade, tumor size, patient age, tumor stage and nodal status of the patient. 
     
     
         16 . The method of  claim 1 , further comprising creating a report summarizing the data obtained by the analysis of said IHA marker expression levels. 
     
     
         17 . The method of  claim 16 , wherein said report includes prediction of the likelihood of long term survival of said patient without the recurrence of breast or ovarian cancer following treatment of the primary tumor. 
     
     
         18 . The method of  claim 16 , wherein said report includes recommendation for a treatment modality of said patient. 
     
     
         19 . The method of  claim 1 , wherein said patient is diagnosed with breast, ovarian or prostate cancer and is undergoing treatment for cancer. 
     
     
         20 . The method of  claim 1 , wherein said patient was diagnosed with breast cancer, ovarian or prostate cancer and has completed treatment for cancer. 
     
     
         21 . The method of  claim 1 , wherein said patient has been diagnosed with breast, ovarian or prostate cancer and is in remission. 
     
     
         22 . A kit for practicing the method of  claim 1 . 
     
     
         23 . The kit as claimed in  claim 22  for analyzing expression levels of at least two IHA marker protein levels in said sample, said kit comprising antibodies immunologically specific for said markers or fragments thereof, means for detecting immune complex formation between said markers and said antibodies and instructional materials comprising ranges of expression levels associated with aggressive metastatic breast cancer and ranges of expression levels associated with non-aggressive non metastatic breast cancer. 
     
     
         24 . A kit as claimed in  claim 22  for analyzing expression levels of at least two IHA marker nucleic acids or information sequence fragments thereof in said sample, said kit comprising nucleic acids which specifically hybridize to said at least two IHA encoding nucleic acids, means for detecting hybridization between said hybridizing nucleic acids and instructional materials comprising ranges of expression levels associated with aggressive metastatic breast cancer and ranges of expression levels associated with non-aggressive non metastatic breast cancer. 
     
     
         25 . The kit of  claim 23  or  24 , wherein said at least two markers are selected from the group consisting of ferroportin/hepcidin, HFE/TFRC, CYBRD1/TFRC_and CYBRD1/SCARA5. 
     
     
         26 . The kit of  claim 23  comprising antibodies immunologically specified for proteins encoded by nucleic acids of the iron regulatory gene signature. 
     
     
         27 . The kit of  claim 24  comprising nucleic acids which hybridize to IHA marker encoding nucleic acids in the iron regulatory gene signature set forth in Table III. 
     
     
         28 . The kit of  claim 23  comprising antibodies immunologically specific for all of the IHA marker proteins listed in Table II. 
     
     
         29 . The kit of  claim 24  comprising nucleic acids which specifically hybridize with each of the IHA marker nucleic acids listed in Table II. 
     
     
         30 . A kit as claimed in  claim 22  for analyzing Ferroportin, CYBRD1, STEAP1, STEAP2, ISCU and TFRC protein levels in said sample, said kit comprising antibodies immunologically specific for Ferroportin, CYBRD1, STEAP1, STEAP2, ISCU and TFRC or fragments thereof, means for detecting immune complex formation between said Ferroportin, CYBRD1, STEAP1, STEAP2, ISCU and TFRC and said antibodies and instructional materials comprising ranges of expression levels associated with aggressive metastatic breast cancer and ranges of expression levels associated with non-aggressive non metastatic breast cancer. 
     
     
         31 . A kit as claimed in  claim 22  for analyzing Ferroportin, CYBRD1, STEAP1, STEAP2, ISCU and TFRC nucleic acid levels in said sample, said kit comprising nucleic acids which specifically hybridize to Ferroportin, CYBRD1, STEAP1, STEAP2, ISCU and TFRC encoding nucleic acids, means for detecting hybridization between said Ferroportin, CYBRD1, STEAP1, STEAP2, ISCU and TFRC nucleic acids and instructional materials comprising ranges of expression levels associated with aggressive metastatic breast cancer and ranges of expression levels associated with non-aggressive non metastatic breast cancer. 
     
     
         32 . A kit as claimed in  claim 22  for analyzing CYBRD1, SCARA5, STEAP1, STEAP2, SFXN1 and ISCU protein levels in said sample, said kit comprising antibodies immunologically specific for CYBRD1, SCARA5, STEAP1, STEAP2, SFXN1 and ISCU. or fragments thereof, means for detecting immune complex formation between said CYBRD1, SCARA5, STEAP1, STEAP2, SFXN1 and ISCU and said antibodies and instructional materials comprising ranges of expression levels associated with aggressive metastatic breast cancer and ranges of expression levels associated with non-aggressive non metastatic breast cancer. 
     
     
         33 . A kit as claimed in  claim 22  for analyzing CYBRD1, SCARA5, STEAP1, STEAP2, SFXN1 and ISCU nucleic acid levels in said sample, said kit comprising nucleic acids which specifically hybridize to CYBRD1, SCARA5, STEAP1, STEAP2, SFXN1 and ISCU encoding nucleic acids, means for detecting hybridization between said CYBRD1, SCARA5, STEAP1, STEAP2, SFXN1 and ISCU nucleic acids and instructional materials comprising ranges of expression levels associated with aggressive metastatic breast cancer and ranges of expression levels associated with non-aggressive non metastatic breast cancer. 
     
     
         34 . A method for identifying agents which modulate iron homeostasis, comprising:
 a) contacting a cell comprising at least one iron homeostasis related protein;   b) assessing the effect of said agent on modulation of iron homeostasis relative to untreated cells.   
     
     
         35 . The method of  claim 34 , wherein said cells are cancer cells selected from the group consisting of breast cancer cells, ovarian cancer cells, prostate cancer cells and blood cells. 
     
     
         36 . The method of  claim 35 , wherein said iron homeostasis related protein is selected from the group consisting of at least one of protein listed in Table II. 
     
     
         37 . The method of  claim 36  wherein modulatory effects of said agent are assessed on a parameter selected from the group consisting of iron transport, iron metabolism, alterations in cellular iron levels, alterations in cellular morphology, proliferation rate or programmed cell death is determined. 
     
     
         38 . A method of predicting the likelihood of long-term survival of a prostate cancer patient without the recurrence of cancer, comprising:
 a) analyzing expression levels of at least two iron homeostasis-associated (IHA) markers in a prostate tissue sample obtained from said patient;   b) comparing the expression level of said IHA markers to previously determined levels in patient cohorts of known outcome, and assigning said patient to a risk group based on correlation with IHA expression levels observed in previously analyzed patient cohorts of known outcome, thereby predicting said patients risk of cancer recurrence.   
     
     
         39 . The method of  claim 38  wherein at least one IHA marker is ferroportin, reduced expression of ferroportin being associated with primary and metastatic prostate cancer. 
     
     
         40 . The method of  claim 38 , further comprising creating a report summarizing the data obtained by said analysis. 
     
     
         41 . The method of  claim 40 , wherein said report includes prediction of the likelihood of long term survival of said patient without the recurrence of prostate cancer following treatment of the primary tumor. 
     
     
         42 . The method of  claim 40 , wherein said report includes recommendation for a treatment modality of said patient. 
     
     
         43 . The method of  claim 42 , wherein said patient is diagnosed with prostate cancer and is undergoing treatment for prostate cancer. 
     
     
         44 . The method of  claim 42 , wherein said patient was diagnosed with prostate cancer and has completed treatment for cancer. 
     
     
         45 . The method of  claim 42 , wherein said patient has been diagnosed with prostate cancer and is in remission. 
     
     
         46 . A kit for practicing the method of  claim 38 .