Methods for Diagnosing Prostate Cancer using MicroRNAs

Abstract

Described herein are methods for diagnosing prostate 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 prostate cancer, comprising:
 obtaining a nucleic acid-containing test sample from a subject suspected of having prostate cancer, wherein the sample is derived from prostate cells;   measuring, by hybridization assay, a level of at least one miR gene product in the test sample; wherein the miR is selected from the group consisting of: let-7d; miR-128a prec; miR-195; miR-203; let-7a-2 prec; miR-34a; miR-20a; miR-218-2; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1 prec; miR-32; miR-206; miR-184 prec; miR-29a prec; miR-29b-2; miR-149; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-24-1; miR-106a; and miR-199a-1;   comparing the level of at least one miR gene product in the test sample to a control level of non-cancerous prostate cells of at least one corresponding miR gene product; and   diagnosing the subject as having prostate cancer, if either
 the level of the at least one miR gene product in the test sample from the subject is greater than the control level for the corresponding miR gene product, wherein the miR is selected from the group consisting of: let-7d; miR-195; miR-203; miR-34a; miR-20a; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-106a; and miR-199a-1; or 
 the level of the at least one miR gene product in the test sample from the subject is lower than the control level for the corresponding miR gene product, wherein the miR is selected from the group consisting of: miR-128a prec; let-7a-2 prec; miR-218-2; miR-29a prec; miR-149; and miR-24-1. 
   
     
     
         2 . A method of diagnosing a subject having prostate cancer, comprising:
 a.) reverse transcribing at least one miR gene product from a nucleic acid-containing test sample from prostate tissue of the subject to provide at least one corresponding miR gene product target oligonucleotide;   b.) hybridizing the at least one corresponding miR gene product target oligonucleotide to a microarray comprising miRNA-specific probe oligonucleotides that include at least one corresponding miRNA-specific probe oligonucleotides, specific for a miR selected from the group consisting of: let-7d; miR-128a prec; miR-195; miR-203; let-7a-2 prec; miR-34a; miR-20a; miR-218-2; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1 prec; miR-32; miR-206; miR-184 prec; miR-29a prec; miR-29b-2; miR-149; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-24-1; miR-106a; and miR-199a-1 to provide a miR-hybridization profile for the test sample;   c.) comparing the test sample miR-hybridization profile to at least one miR control hybridization profile of normal prostate tissue; and   d.) diagnosing the subject as having prostate cancer if either:
 i. the level of at least one miR gene product in the test sample is greater than the control level of corresponding miR gene product, wherein the miR is selected from the group consisting of: let-7d; miR-195; miR-203; miR-34a; miR-20a; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-106a; and miR-199a-1; or 
 ii. the level of at least one miR gene product in the test sample is less than the control level of corresponding miR gene product, wherein the miR is selected from the group consisting of: miR-128a prec; let-7a-2 prec; miR-218-2; miR-29a prec; miR-149; and miR-24-1. 
   
     
     
         3 . A method of diagnosing prostate cancer, comprising:
 measuring, by hybridization assay, the level of at least one miR gene product in a test sample from prostate cells of a subject;   comparing the measured level of at the least one miR gene product in a test sample from a subject to a control level of non-cancerous prostate cells for the at least one miR gene product; and   diagnosing the subject as having prostate cancer, if the level of the at least one miR gene product in the test sample from the subject is greater than the control level of miR gene product, wherein the miR is selected from the group consisting of: let-7d; miR-195; miR-203; miR-34a; miR-20a; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-106a; and miR-199a-1.   
     
     
         4 . A method of diagnosing a subject having prostate cancer, comprising:
 a.) reverse transcribing at least one miR gene product from a test sample derived from prostate cells of a subject to provide at least one corresponding miR gene product target oligonucleotide;   b.) hybridizing the at least one miR gene product target oligonucleotide to a microarray comprising miRNA-specific probe oligonucleotides that include at least one corresponding miR specific probe oligonucleotide to provide a miR hybridization profile for the test sample;   c.) comparing the test sample miR hybridization profile to at least one control miR hybridization profile, wherein the control is derived from miRNA expression of non-cancerous prostate cells; and   d.) diagnosing the subject as having prostate cancer if the level of at least one miR gene product in the hybridization profile from the test sample is greater than the level of corresponding miR gene product in the hybridization profile from the control miR hybridization profile, wherein the miR is selected from the group consisting of: let-7d; miR-195; miR-203; miR-34a; miR-20a; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-106a; and miR-199a-1.   
     
     
         5 . A method for detecting likelihood of prostate cancer in a subject, the method comprising:
 detecting one or both of the presence and amount of one or more biomarkers in a biological sample comprised of prostate cells from the subject, wherein at least one of the biomarkers is a miR gene product, wherein the miR is selected from the group consisting of: let-7d; miR-128a prec; miR-195; miR-203; let-7a-2 prec; miR-34a; miR-20a; miR-218-2; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1 prec; miR-32; miR-206; miR-184 prec; miR-29a prec; miR-29b-2; miR-149; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-24-1; miR-106a; and miR-199a-1; and   classifying the subject as likely to have prostate cancer if the amount of the miR gene product is altered in the biological sample as compared to a non-prostate cancer reference amount of a corresponding miR gene product biomarker.   
     
     
         6 . A method of facilitating a diagnosis of a prostate cancer in a subject, comprising:
 obtaining a test sample from prostate cells of the subject;   measuring a level of expression of at least one miR, wherein the miR is selected from the group consisting of: let-7d; miR-195; miR-203; miR-34a; miR-20a; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-106a; and miR-199a-1; and   comparing the level of the at least one miR with a corresponding pre-determined level for the at least one miR, the pre-determined level being obtained from a control sample from a control subject who has prostate cancer, wherein having a level of at least one miR, wherein the miR is selected from the group consisting of: let-7d; miR-195; miR-203; miR-34a; miR-20a; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-106a; and miR-199a-1, that is at or above the corresponding predetermined level indicates that the subject has prostate cancer.   
     
     
         7 . The method of  claim 1 , wherein the subject is a human. 
     
     
         8 . The method of  claim 1 , further comprising:
 confirming a diagnosis of prostate cancer by measuring at least one additional miR gene product, wherein the miR is wherein the miR is selected from the group consisting of: let-7d; miR-128a prec; miR-195; miR-203; let-7a-2 prec; miR-34a; miR-20a; miR-218-2; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1 prec; miR-32; miR-206; miR-184 prec; miR-29a prec; miR-29b-2; miR-149; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-24-1; miR-106a; and miR-199a-1;   comparing the level of the at least one additional miR gene product in the test sample from a subject to a control level of at least one corresponding miR gene product; and   confirming the diagnosing of the subject as having prostate cancer, if the level of the at least one additional miR gene product in the test sample from the subject is altered relative to the control level of the corresponding miR gene product, wherein an increase or decrease in the level of additional miR gene product in the test sample, relative to the control level of gene product, is indicative of the subject having prostate cancer.   
     
     
         9 . The method of  claim 1 , further comprising
 confirming a diagnosis of prostate cancer by measuring at least one additional miR gene product, wherein the miR is selected from the group consisting of: miR-128a prec; let-7a-2 prec; miR-218-2; miR-29a prec; miR-149; and miR-24-1;   comparing the level of the at least one additional miR gene product in the test sample from a subject to a control level of at least one corresponding miR gene product; and   confirming the diagnosing of the subject as having prostate cancer, if the level of the at least one additional miR gene product in the test sample from the subject is low relative to the control level of the corresponding miR gene product, wherein a decrease in the level of additional miR gene product in the test sample, relative to the control level of gene product, is indicative of the subject having prostate cancer.   
     
     
         10 . The method of  claim 1 , further comprising:
 communicating the diagnosis to at least one person.   
     
     
         11 . The method of  claim 1 , wherein a miR signature of prostate cancer consists essentially of: let-7d; miR-195; miR-203; miR-34a; miR-20a; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-106a; and miR-199a-1; wherein each miR in the signature is upregulated. 
     
     
         12 . The method of  claim 1 , further comprising:
 distinguishing prostate cancer from a non-prostate cancer by comparing the level of at least one additional miR gene product in a test sample from the subject to the control level of the miR gene product, wherein the at least one additional miR gene product is selected from the group consisting of: one or more miRs commonly up-regulated in non-prostate solid cancers selected from the group consisting of: miR-17-5p; miR-29b-2; miR-128b; miR-199a-1; miR-146; miR-155; miR-181b-1; miR-20a; miR-32; miR-30c; and miR-106a; and, diagnosing the subject as not having prostate cancer if the compared level high is high for the at least one additional miR gene product.   
     
     
         13 . The method of  claim 1 , further comprising:
 comparing the level of at least one additional miR gene product in a test sample from the subject to the control level of the at least one additional miR gene product, wherein the at least one additional miR gene product is selected from the group consisting of: let-7d; miR-128a prec; miR-195; miR-203; let-7a-2 prec; miR-34a; miR-20a; miR-218-2; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1 prec; miR-32; miR-206; miR-184 prec; miR-29a prec; miR-29b-2; miR-149; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-24-1; miR-106a; and miR-199a-1;   confirming the diagnosis of prostate cancer if:
 the compared level is high, as compared to a control level for any one or more of: let-7d; miR-195; miR-203; miR-34a; miR-20a; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-106a; and miR-199a-1, or 
 the compared level is low, as compared to a control level, for any one or more of: miR-128a prec; let-7a-2 prec; miR-218-2; miR-29a prec; miR-149; and miR-24-1. 
   
     
     
         14 . The method of  claim 1 , further comprising:
 comparing the level of at least two additional miR gene products in a test sample from the subject to a control level of the corresponding miR gene products, wherein the at least two additional miR gene products are selected from the group consisting of: let-7d; miR-128a prec; miR-195; miR-203; let-7a-2 prec; miR-34a; miR-20a; miR-218-2; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1 prec; miR-32; miR-206; miR-184 prec; miR-29a prec; miR-29b-2; miR-149; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-24-1; miR-106a; and miR-199a-1.   
     
     
         15 . The method of  claim 1 , further comprising:
 comparing the level of at least three additional miR gene products in a test sample from the subject to a control level of the corresponding miR gene products, wherein the at least three additional miR gene products are selected from the group consisting of: let-7d; miR-128a prec; miR-195; miR-203; let-7a-2 prec; miR-34a; miR-20a; miR-218-2; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1 prec; miR-32; miR-206; miR-184 prec; miR-29a prec; miR-29b-2; miR-149; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-24-1; miR-106a; and miR-199a-1.   
     
     
         16 . The method of  claim 1 , further comprising:
 comparing the level of at least four additional miR gene products in a test sample from the subject to a control level of the corresponding miR gene products, wherein the at least four additional miR gene products are selected from the group consisting of: let-7d; miR-128a prec; miR-195; miR-203; let-7a-2 prec; miR-34a; miR-20a; miR-218-2; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1 prec; miR-32; miR-206; miR-184 prec; miR-29a prec; miR-29b-2; miR-149; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-24-1; miR-106a; and miR-199a-1.   
     
     
         17 . The method of  claim 2 , further comprising:
 comparing a hybridization profile of at least one additional miR gene product in the test sample from the subject to the control hybridization profile from of the miR gene product, wherein the at least one additional miR gene product is selected from the group consisting of: let-7d; miR-128a prec; miR-195; miR-203; let-7a-2 prec; miR-34a; miR-20a; miR-218-2; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1 prec; miR-32; miR-206; miR-184 prec; miR-29a prec; miR-29b-2; miR-149; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-24-1; miR-106a; and miR-199a-1;
 wherein upregulated expression, as compared to a control, of let-7d; miR-195; miR-203; miR-34a; miR-20a; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-106a; and miR-199a-1, or 
 non-upregulated expression, as compared to a control, of miR-128a prec; let-7a-2 prec; miR-218-2; miR-29a prec; miR-149; and miR-24-1, in the test sample confirms a diagnosis of prostate cancer. 
   
     
     
         18 . A method of inhibiting tumorigenesis in a subject who has prostate cancer, comprising:
 determining the amount of at least one miR gene product in cancer cells from the subject, relative to control; and   altering the amount of miR gene product in the cancer cells by:
 (i) administering to the subject an effective amount of at least one isolated or synthetic miR gene product, or an isolated variant or biologically-active fragment thereof, wherein the miR is selected from the group consisting of: miR-128a prec; let-7a-2 prec; miR-218-2; miR-29a prec; miR-149; and miR-24-1; or 
 (ii) administering to the subject an effective amount of at least one compound for inhibiting expression of the at least one miR gene product, wherein the miR is selected from the group consisting of: let-7d; miR-195; miR-203; miR-34a; miR-20a; miR-29a; miR-25; miR-95; miR-197; miR-135-2; miR-187; miR-196-1; miR-148; miR-191; miR-21; let-7i; miR-198; miR-199a-2; miR-30c; miR-17-5p; miR-92-2; miR-146; miR-181b-1; miR-196-1; miR-93-1; miR-223; miR-16-1; miR-101-1 prec; miR-124a-1; miR-26a-1; miR-214; miR-27a; miR-106a; and miR-199a-1,
 such that tumorigenesis is inhibited in the subject.