Methods for Diagnosing Breast Cancer Using MicroRNAs

Abstract

Described herein are methods for diagnosing breast cancer using microRNAs. Also described are methods and compositions for the diagnosis and treatment of solid cancers. Methods of identifying inhibitors of tumorigenesis are also provided.

What is claimed is: 
     
         1 . A method of diagnosing whether a subject has, or is at risk for developing, breast cancer, comprising:
 extracting a test sample from a subject having, or suspected of having, breast cancer, wherein the sample is extracted from breast tissue;   measuring, by hybridization assay, the level of at least one miR gene product in the test sample;   comparing the level of the at least one miR gene product in the test sample to the level of at least one corresponding miR gene product in a control sample;   correlating a decrease in the test sample level of the at least one miR gene product compared to the level of a corresponding miR gene product in the control sample with a subject having, or being at risk for developing, breast cancer; and   diagnosing the subject as having, or being at risk for developing, breast cancer, if the level of the at least one miR gene product in the test sample from the subject is less than the level of the corresponding miR gene product in the control sample;   wherein a decrease in the level of the at least one miR gene product in the test sample, relative to the control level of the corresponding miR gene product, is indicative of the subject having, or being at risk for developing, breast cancer; and   wherein the at least one miR gene product comprises one or more of: miR-10b, miR-125b-2, miR-125b-1, miR-145, miR-140, miR-130a, let-7a-2, miR-205, miR-224, miR-100, miR-30c, and miR-16-2.   
     
     
         2 . The method of  claim 1 , wherein the at least one miR gene product consists essentially of miR-10b. 
     
     
         3 . The method of  claim 2 , which further comprises comparing the level of at least one additional miR gene product in the test sample from the subject to a control level of a corresponding miR gene product, wherein the at least one additional miR gene product is selected from the group consisting of: miR-125b-2, miR-125b-1, miR-145, miR-140, miR-130a, let-7a-2, miR-205, miR-224, miR-100, miR-30c, and miR-16-2. 
     
     
         4 . The method of  claim 2 , which further comprises comparing the level of at least one additional miR gene product in the test sample from the subject to a control level of a corresponding miR gene product, wherein the at least one additional miR gene product is selected from the group consisting of: miR-21, miR-146, miR-181a, miR-213, miR-29a prec, miR-181b-1, miR-199b, miR-29b-1, miR-155, miR-29c, miR-31, miR-17-5p, miR-210, and miR-122a. 
     
     
         5 . The method of  claim 2 , which further comprises comparing the level of at least two additional miR gene products in the test sample from the subject to a control level of corresponding miR gene products, wherein the at least two additional miR gene products are selected from the group consisting of: miR-125b-2, miR-125b-1, miR-145, miR-140, miR-130a, let-7a-2, miR-205, miR-224, miR-100, miR-30c, miR-16-2, miR-21, miR-146, miR-181a, miR-213, miR-29a prec, miR-181b-1, miR-199b, miR-29b-1, miR-155, miR-29c, miR-31, miR-17-5p, miR-210, and miR-122a. 
     
     
         6 . The method of  claim 2 , which further comprises comparing the level of at least three additional miR gene products in the test sample from the subject to a control level of corresponding miR gene products, wherein the at least three additional miR gene products are selected from the group consisting of: miR-125b-2, miR-125b-1, miR-145, miR-140, miR-130a, let-7a-2, miR-205, miR-224, miR-100, miR-30c, miR-16-2, miR-21, miR-146, miR-181a, miR-213, miR-29a prec, miR-181b-1, miR-199b, miR-29b-1, miR-155, miR-29c, miR-31, miR-17-5p, miR-210, and miR-122a. 
     
     
         7 . A method of diagnosing whether a subject has, or is at risk for developing, breast cancer, comprising:
 obtaining a test sample from a subject having, or suspected of having, breast cancer, wherein the test sample comprises breast tissue;   reverse transcribing at least miR-10b gene product from the test sample to provide at least one corresponding miR gene product target oligonucleotides;   hybridizing at least miR-10b target oligonucleotides to a microarray comprising miRNA-specific probe oligonucleotides that include at least one corresponding miR-10b miRNA-specific probe oligonucleotides to provide a hybridization profile for the test sample;   comparing the signal of the at least miR-10b in the test sample hybridization profile to the signal of a corresponding miRNA in a control hybridization profile;   correlating an increase in the signal of the at least miR-10b in the test sample hybridization profile compared to the signal of the control hybridization profile with a subject having, or being at risk for developing, breast cancer; and   diagnosing the subject as having, or being at risk for developing, breast cancer if the level of the at least one miR gene product in the hybridization profile from the test sample is less than the control level of miR-10b gene product;   wherein a decrease in the level of miR-10b gene product in the test sample, relative to the control level of miR-10b gene product, is indicative of the subject having, or being at risk for developing, breast cancer.   
     
     
         8 . The method of  claim 7 , which further comprises comparing a hybridization profile of at least one additional miR gene product in the test sample from the subject to a control hybridization profile of the corresponding miR gene product, wherein the at least one additional miR gene product is selected from the group consisting of: miR-125b-2, miR-125b-1, miR-145, miR-140, miR-130a, let-7a-2, miR-205, miR-224, miR-100, miR-30c, and miR-16-2. 
     
     
         9 . The method of  claim 7 , which further comprises comparing a hybridization profile of at least one additional miR gene product in the test sample from the subject to a control hybridization profile of a corresponding miR gene product, wherein the at least one additional miR gene product is selected from the group consisting of: miR-21, miR-146, miR-181a, miR-213, miR-29a prec, miR-181b-1, miR-199b, miR-29b-1, miR-155, miR-29c, miR-31, miR-17-5p, miR-210, and miR-122a. 
     
     
         10 . The method of  claim 7 , which further comprises comparing a hybridization profile of at least two additional miR gene products in the test sample from the subject to a control hybridization profile of corresponding miR gene products, wherein the at least two additional miR gene products are selected from the group consisting of: miR-125b-2, miR-125b-1, miR-145, miR-140, miR-130a, let-7a-2, miR-205, miR-224, miR-100, miR-30c, miR-16-2, miR-21, miR-146, miR-181a, miR-213, miR-29a prec, miR-181b-1, miR-199b, miR-29b-1, miR-155, miR-29c, miR-31, miR-17-5p, miR-210, and miR-122a. 
     
     
         11 . The method of  claim 7 , which further comprises comparing a hybridization profile of at least three additional miR gene products in the test sample from the subject to a control hybridization profile of corresponding miR gene products, wherein the at least three additional miR gene products are selected from the group consisting of: miR-125b-2, miR-125b-1, miR-145, miR-140, miR-130a, let-7a-2, miR-205, miR-224, miR-100, miR-30c, miR-16-2, miR-21, miR-146, miR-181a, miR-213, miR-29a prec, miR-181b-1, miR-199b, miR-29b-1, miR-155, miR-29c, miR-31, miR-17-5p, miR-210, and miR-122a. 
     
     
         12 . A method of diagnosing whether a subject has, or is at risk for developing, breast cancer, comprising:
 extracting a test sample from a subject having, or suspected of having, breast cancer, wherein the sample is extracted from breast tissue;   measuring, by hybridization assay, the level of at least one miR gene product in the test sample;   comparing the level of the at least one miR gene product in the test sample to the level of at least one corresponding miR gene product in a control sample;   correlating an increase in the test sample level of the at least one miR gene product compared to the level of a corresponding miR gene product in the control sample with a subject having, or being at risk for developing, breast cancer; and   diagnosing the subject as having, or being at risk for developing, breast cancer, if the level of the at least one miR gene product in the test sample from the subject is greater than the level of the corresponding miR gene product in the control sample;   wherein an increase in the level of the at least one miR gene product in the test sample, relative to the control level of the at least one corresponding miR gene product, is indicative of the subject having, or being at risk for developing, breast cancer; and   wherein the at least one miR gene product comprises one or more of: miR-210, miR-21, miR-29b-2, miR-146, miR-181a, miR-213, miR-29a prec, miR-181b-1, miR-199b, miR-29b-1, miR-155, miR-29c, miR-31, miR-17-5p, and miR-122a.   
     
     
         13 . The method of  claim 12 , wherein the at least one miR gene product consists essentially of miR-31. 
     
     
         14 . The method of  claim 13 , which further comprises comparing the level of at least one additional miR gene product in the test sample from the subject to a control level of a corresponding miR gene product, wherein the at least one additional miR gene product is selected from the group consisting of: miR-21, miR-29b-2, miR-146, miR-181a, miR-213, miR-29a prec, miR-181b-1, miR-199b, miR-29b-1, miR-155, miR-29c, miR-17-5p, miR-210, and miR-122a. 
     
     
         15 . The method of  claim 13 , which further comprises comparing the level of at least one additional miR gene product in the test sample from the subject to a control level of a corresponding miR gene product, wherein the at least one additional miR gene product is selected from the group consisting of: miR-125b-2, miR-125b-1, miR-145, miR-140, miR-130a, let-7a-2, miR-205, miR-224, miR-100, miR-30c, and miR-16-2. 
     
     
         16 . The method of  claim 13 , which further comprises comparing the level of at least two additional miR gene products in the test sample from the subject to a control level of corresponding miR gene products, wherein the at least two additional miR gene products are selected from the group consisting of: miR-125b-2, miR-125b-1, miR-145, miR-140, miR-130a, let-7a-2, miR-205, miR-224, miR-100, miR-30c, miR-16-2, miR-21, miR-29b-2, miR-146, miR-181a, miR-213, miR-29a prec, miR-181b-1, miR-199b, miR-29b-1, miR-155, miR-29c, miR-17-5p, miR-210, and miR-122a. 
     
     
         17 . The method of  claim 12 , wherein the at least one miR gene product consists essentially of miR-210. 
     
     
         18 . The method of  claim 12 , wherein the at least one miR gene product consists essentially of miR-122a. 
     
     
         19 . A method of diagnosing whether a subject has, or is at risk for developing, breast cancer, comprising:
 obtaining a test sample from a subject having, or suspected of having, breast cancer, wherein the test sample comprises breast tissue;   reverse transcribing at least miR-31 gene product from the test sample to provide at least one corresponding miR gene product target oligonucleotides;   hybridizing at least miR-31 target oligonucleotides to a microarray comprising miRNA-specific probe oligonucleotides that include at least one corresponding miR-31 miRNA-specific probe oligonucleotides to provide a hybridization profile for the test sample;   comparing the signal of the at least miR-31 in the test sample hybridization profile to the signal of a corresponding miRNA in a control hybridization profile;   correlating an increase in the signal of the at least miR-31 in the test sample hybridization profile compared to the signal of the control hybridization profile with a subject having, or being at risk for developing, breast cancer; and   diagnosing the subject as having, or being at risk for developing, breast cancer if the level of at least one miR gene product in the hybridization profile from the test sample is greater than the control level of miR-31 gene product;   wherein an increase in the level of miR-31 gene product in the test sample, relative to the control level of miR-31 gene product, is indicative of the subject having, or being at risk for developing, breast cancer.   
     
     
         20 . The method of  claim 19 , which further comprises comparing a hybridization profile of at least one additional miR gene product in the test sample from the subject to a control hybridization profile of the corresponding miR gene product, wherein the at least one additional miR gene product is selected from the group consisting of: miR-21, miR-29b-2, miR-146, miR-181a, miR-213, miR-29a prec, miR-181b-1, miR-199b, miR-29b-1, miR-155, miR-29c, miR-17-5p, miR-210, and miR-122a. 
     
     
         21 . The method of  claim 19 , which further comprises comparing a hybridization profile of at least one additional miR gene product in the test sample from the subject to a control hybridization profile of the corresponding miR gene product, wherein the at least one additional miR gene product is selected from the group consisting of: miR-125b-2, miR-125b-1, miR-145, miR-140, miR-130a, let-7a-2, miR-205, miR-224, miR-100, miR-30c, and miR-16-2. 
     
     
         22 . The method of  claim 19 , which further comprises comparing a hybridization profile of at least two additional miR gene products in the test sample from the subject to a control hybridization profile of the corresponding miR gene products, wherein the at least two additional miR gene products are selected from the group consisting of: miR-125b-2, miR-125b-1, miR-145, miR-140, miR-130a, let-7a-2, miR-205, miR-224, miR-100, miR-30c, miR-16-2, miR-21, miR-29b-2, miR-146, miR-181a, miR-213, miR-29a prec, miR-181b-1, miR-199b, miR-29b-1, miR-155, miR-29c, miR-17-5p, miR-210, and miR-122a.