MicroRNA-Based Methods and Compositions for the Diagnosis, Prognosis and Treatment of Ovarian Cancer Using a Real-Time PCR Platform

Abstract

Methods and compositions for the diagnosis, prognosis and/or treatment of ovarian cancer are disclosed.

1 . A method of diagnosing whether a subject has, or is at risk for developing, an epithelial ovarian cancer, comprising
 measuring the level of at least one biomarker in a test sample of serum from the subject, wherein the at least one biomarker differentially expressed between tumor tissue and non-tumor tissue comprises miR-21; and   wherein an increase in the level of the miR-21 biomarker in the test sample, relative to the level of a corresponding biomarker in a control sample, is indicative of the subject either having, or being at risk for developing, epithelial ovarian cancer.   
     
     
         2 . The method of  claim 1 , wherein the at least one additional biomarker is one or more of miR-92, miR-93, miR-126, miR-29a, miR-155, miR-127 and miR-99b, or functional variants thereof. 
     
     
         3 . (canceled) 
     
     
         4 . The method of  claim 2 , wherein the at least one additional biomarker is over-expressed, and wherein the at least one additional over-expressed biomarker is selected from the group consisting of: miR-92, miR-93, miR-126 and miR-29a, or functional variants thereof. 
     
     
         5 . (canceled) 
     
     
         6 . The method of  claim 2 , wherein the level of the at least one additional biomarker in the test sample is less than the level of the corresponding biomarker in the control sample, wherein the at least one biomarker is one or more of miR-155, miR-127 and miR-99b, or functional variants thereof. 
     
     
         7 . (canceled) 
     
     
         8 . A method of screening for one or more biomarkers for ovarian cancer in a subject, comprising:
 obtaining a sample of serum from the subject,   conducting quantitative real-time polymerase chain reaction (RT-PCR), and   quantifying one or more one biomarkers differentially expressed between tumor tissue and non-tumor tissue, wherein the biomarkers are selected from one or more of miR-21, miR-92, miR-93, miR-126, miR-29a, miR-155, miR-127 and miR-99b, or functional variants thereof.   
     
     
         9 . (canceled) 
     
     
         10 . (canceled) 
     
     
         11 . A biomarker for ovarian cancer, comprising at least one biomarker differentially expressed between tumor tissue and non-tumor tissue, wherein the biomarkers are selected from one or more of miR-21, miR-92, miR-93, miR-126, miR-29a, miR-155, miR-127 and miR-99b, or functional variants thereof. 
     
     
         12 . (canceled) 
     
     
         13 . (canceled) 
     
     
         14 . (canceled) 
     
     
         15 . (canceled) 
     
     
         16 . (canceled) 
     
     
         17 . (canceled) 
     
     
         18 . (canceled) 
     
     
         19 . (canceled) 
     
     
         20 . (canceled) 
     
     
         21 . (canceled) 
     
     
         22 . (canceled) 
     
     
         23 . (canceled) 
     
     
         24 . (canceled) 
     
     
         25 . (canceled) 
     
     
         26 . (canceled) 
     
     
         27 . (canceled) 
     
     
         28 . (canceled) 
     
     
         29 . (canceled) 
     
     
         30 . (canceled) 
     
     
         31 . (canceled) 
     
     
         32 . (canceled) 
     
     
         33 . (canceled) 
     
     
         34 . (canceled) 
     
     
         35 . (canceled) 
     
     
         36 . (canceled) 
     
     
         37 . (canceled) 
     
     
         38 . A method for determining the prognosis of a subject with ovarian cancer, comprising measuring the level of at least one biomarker in a test sample of serum from the subject,
 wherein the biomarker is selected from one or more of miR-21, miR92, miR-93, miR-126, miR-29a, miR-155, miR-127 and miR-99b, or functional variants thereof, and   wherein: i) the biomarker is associated with an adverse prognosis in ovarian cancer; and ii) an alteration in the level of the at least one biomarker in the test sample, relative to the level of a corresponding biomarker in a control sample, is indicative of an adverse prognosis.   
     
     
         39 . The method of  claim 38 , comprising:
 a) reverse transcribing RNA from the test sample of serum obtained from the subject to provide a set of target oligodeoxynucleotides;   b) hybridizing the target oligodeoxynucleotides to a microarray comprising miRNA-specific probe oligonucleotides to provide a hybridization profile for the test sample; and   c) comparing the test sample hybridization profile to a hybridization profile generated from a control sample, wherein an alteration in the signal of at least one biomarker is indicative of the subject either having, or being at risk for developing, ovarian cancer.   
     
     
         40 . The method of  claim 38 , wherein the signal of at least miR-155, miR-127 and miR-99, relative to the signal generated from the control sample, is down-regulated, and/or wherein the signal of at least miR-21, miR92, miR-93, miR-126, miR-29a, relative to the signal generated from the control sample, is up-regulated. 
     
     
         41 . (canceled) 
     
     
         42 . (canceled) 
     
     
         43 . (canceled) 
     
     
         44 . (canceled) 
     
     
         45 . (canceled) 
     
     
         46 . (canceled) 
     
     
         47 . (canceled) 
     
     
         48 . (canceled) 
     
     
         49 . (canceled) 
     
     
         50 . (canceled) 
     
     
         51 . (canceled) 
     
     
         52 . (canceled) 
     
     
         53 . A kit for screening for epithelial ovarian cancer, wherein the kit comprises: one or more reagents of at least one biomarker selected from one or more of: miR-21, miR-92, miR-93, miR-126, miR-29a, miR-155, miR-127 and miR-99b, or functional variants thereof. 
     
     
         54 . The kit of  claim 53 , wherein the presence of the biomarker is detected using a reagent comprising an antibody or an antibody fragment which specifically binds with at least one biomarker. 
     
     
         55 . (canceled) 
     
     
         56 . (canceled) 
     
     
         57 . (canceled) 
     
     
         58 . (canceled) 
     
     
         59 . (canceled) 
     
     
         60 . (canceled) 
     
     
         61 . (canceled) 
     
     
         62 . (canceled) 
     
     
         63 . (canceled) 
     
     
         64 . (canceled) 
     
     
         65 . (canceled) 
     
     
         66 . (canceled) 
     
     
         67 . The method of  claim 1 , further comprising collecting a plurality of test samples from the subject at different time points and comparing the amount of the at least one biomarker in each test sample to determine if the amount of the at least one biomarker is increasing or decreasing in the subject over time. 
     
     
         68 . (canceled) 
     
     
         69 . (canceled) 
     
     
         70 . (canceled) 
     
     
         71 . (canceled) 
     
     
         72 . (canceled) 
     
     
         73 . (canceled) 
     
     
         74 . (canceled) 
     
     
         75 . (canceled) 
     
     
         76 . (canceled) 
     
     
         77 . A method for classifying an ovarian tissue from a subject comprising:
 a) measuring the expression of one or more of: miR-21, miR-92, miR-93, miR-126, miR-29a, miR-155, miR-127 and miR-99b, or functional variants thereof, among the miR in a test cell population,   wherein at least one cell in the test cell population is capable of expressing one or more of: miR-21, miR92, miR-93, miR-126, miR-29a, miR-155, miR-127 and miR-99b, or functional variants thereof among the miR;   b) comparing the expression of the miR(s) to the expression of the miR(s) in a reference cell population comprising at least one cell for which an ovarian cancer classification is known; and   c) identifying a difference, if present, in expression levels of one or more miR(s) in the test cell population and reference cell population, thereby classifying the ovarian cancer in the subject.   
     
     
         78 . The method of  claim 77 , wherein a difference in the expression in the test cell population as compared to the reference cell population indicates that the test cell population has a different classification as the cells from the reference cell population. 
     
     
         79 . The method of  claim 77 , wherein a similar expression pattern in the test cell population as compared to the reference cell population indicates that the test cell population has the same classification as the cells from the reference cell population. 
     
     
         80 . The method of  claim 77 , wherein the reference cell population is a plurality of cells or a database. 
     
     
         81 . The method of  claim 80 , wherein the reference cell population is selected from the group consisting of: a reference cell population classified as a cell population from normal ovarian tissue, a reference cell population classified as a cell population from benign ovarian tissue and a reference cell population classified as a cell population from malignant ovarian tissue.