Methods for Diagnosing Pancreatic Cancer Using MicroRNAs

Abstract

Described herein are methods for diagnosing pancreatic 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 pancreatic cancer, comprising:
 a.) obtaining a test sample from a subject having, or suspected of having pancreatic cancer, wherein the sample is derived from pancreas tissue;   b.) measuring, by hybridization assay, the level of at least one miR gene product wherein the miR is selected from the group consisting of: miR-103-2; miR-103-1; miR-24-2; miR-107; miR-100; miR-125b-2; miR-125b-1; miR-24-1; miR-191; miR-23a; miR-26a-1; miR-125a; miR-130a; miR-26b; miR-145; miR-126; miR-16-2; miR-146; miR-214; miR-99b; miR-128b; miR-29b-2; miR-29a; miR-25; miR-16-1; miR-99a; miR-224; miR-30d; miR-92-2; miR-199a-1; miR-223; miR-29c; miR-30b; miR-129-1/2; miR-197; miR-17-5p; miR-30c; miR-7-1; miR-93-1; miR-140; miR-30a-5p; miR-132; miR-181b-1; miR-23b; miR-20a; miR-222; miR-27a; miR-92-1; miR-21; miR-129-1/2 prec; miR-150; miR-32; miR-106a; and miR-29b-1;   c.) comparing the level of at least one miR gene product in the test sample from a subject to a control level of at least one corresponding miR gene product;   d.) diagnosing the subject as having, or at risk for developing, pancreatic 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 the corresponding miR gene product;   wherein an increase in the level of miR gene product in the test sample, relative to the control level of gene product, is indicative of the subject having pancreatic cancer.   
     
     
         2 . A method of diagnosing whether a subject has pancreatic cancer, comprising:
 a.) reverse transcribing at least one miR gene product from a test sample from the subject to provide at least one corresponding miR gene product target oligonucleotides; wherein the test sample is derived from pancreas tissue; and wherein the miR is selected from the group consisting of: miR-103-2; miR-103-1; miR-24-2; miR-107; miR-100; miR-125b-2; miR-125b-1; miR-24-1; miR-191; miR-23a; miR-26a-1; miR-125a; miR-130a; miR-26b; miR-145; miR-126; miR-16-2; miR-146; miR-214; miR-99b; miR-128b; miR-29b-2; miR-29a; miR-25; miR-16-1; miR-99a; miR-224; miR-30d; miR-92-2; miR-199a-1; miR-223; miR-29c; miR-30b; miR-129-1/2; miR-197; miR-17-5p; miR-30c; miR-7-1; miR-93-1; miR-140; miR-30a-5p; miR-132; miR-181b-1; miR-23b; miR-20a; miR-222; miR-27a; miR-92-1; miR-21; miR-129-1/2 prec; miR-150; miR-32; miR-106a; and miR-29b-1;   b.) hybridizing at least one miR target oligodeoxynucleotides to a microarray comprising miRNA-specific probe oligonucleotides that include at least one corresponding miRNA-specific probe oligonucleotides to provide a hybridization profile for the test sample;   c.) comparing the test sample hybridization profile to at least one control hybridization profile; and   d.) diagnosing the subject as having, or at risk for developing, pancreatic cancer if the level of at least one miR gene product in the test sample is greater than the control;   wherein an increase in the level of miR gene product in the test sample, relative to the control level of miR gene product, is indicative of the subject having pancreatic cancer.   
     
     
         3 . The method of  claim 1  for diagnosing pancreatic cancer, comprising:
 obtaining a test sample from subject having, or suspected of having, pancreatic cancer, wherein the sample is extracted from pancreas tissue; 
 measuring, by hybridization assay, the level of at least one miR gene product of each of three miRs, wherein the miRs are selected from the group consisting of: miR-103-2; miR-103-1; miR-24-2; miR-107; miR-100; miR-125b-2; miR-125b-1; miR-24-1; miR-191; miR-23a; miR-26a-1; miR-125a; miR-130a; miR-26b; miR-145; miR-126; miR-16-2; miR-146; miR-214; miR-99b; miR-128b; miR-29b-2; miR-29a; miR-25; miR-16-1; miR-99a; miR-224; miR-30d; miR-92-2; miR-199a-1; miR-223; miR-29c; miR-30b; miR-129-1/2; miR-197; miR-17-5p; miR-30c; miR-7-1; miR-93-1; miR-140; miR-30a-5p; miR-132; miR-181b-1; miR-23b; miR-20a; miR-221; miR-222; miR-27a; miR-92-1; miR-21; miR-129-1/2 prec; miR-150; miR-32; miR-106a; and miR-29b-1; 
 comparing the level of miR gene product of each of miR gene product, in the test sample to a control level of each corresponding miR gene product; and 
 diagnosing the subject as having, or at risk for developing, pancreatic cancer, if the level of miR gene products of each of the three miRs in the test sample are high compared with the control levels of the corresponding miR gene products. 
 
     
     
         4 . A method of diagnosing pancreatic cancer, comprising:
 obtaining a test sample from a subject having, or suspected of having pancreatic cancer, wherein the sample is derived from pancreas tissue;   measuring, by hybridization assay, the level of at least one miR gene product of miR-155 and/or miR-152-prec;   comparing the level of the at least one miR gene product in the test sample from a subject to a control level of at least one corresponding miR gene product; and   diagnosing the subject as having, or at risk for developing, pancreatic cancer, if the level of the at least one 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 miR gene product in the test sample, relative to the control level of gene product, is indicative of the subject having pancreatic cancer.   
     
     
         5 . The method of  claim 2 , further comprising:
 reverse transcribing at least one additional miR gene product; and   diagnosing the subject as having, or at risk for developing, pancreatic cancer if the level of the at least one additional miR gene product in the test sample is greater than the control;   wherein an increase in the level of the miR gene product in the test sample, relative to the control level, is indicative of the subject having pancreatic cancer.   
     
     
         6 . The method of  claim 4 , further comprising:
 confirming diagnosis by measuring at least one additional miR gene product, wherein the miR is selected from the group consisting of: miR-103-2; miR-103-1; miR-24-2; miR-107; miR-100; miR-125b-2; miR-125b-1; miR-24-1; miR-191; miR-23a; miR-26a-1; miR-125a; miR-130a; miR-26b; miR-145; miR-126; miR-16-2; miR-146; miR-214; miR-99b; miR-128b; miR-29b-2; miR-29a; miR-25; miR-16-1; miR-99a; miR-224; miR-30d; miR-92-2; miR-199a-1; miR-223; miR-29c; miR-30b; miR-129-1/2; miR-197; miR-17-5p; miR-30c; miR-7-1; miR-93-1; miR-140; miR-30a-5p; miR-132; miR-181b-1; miR-23b; miR-20a; miR-221; miR-222; miR-27a; miR-92-1; miR-21; miR-129-1/2 prec; miR-150; miR-32; miR-106a; and miR-29b-1;   wherein an increase in the level of the additional gene product in the test sample, relative to a control level of miR gene product, is indicative of the subject having pancreatic cancer.   
     
     
         7 . The method of  claim 1 , further comprising:
 bolstering the diagnosis by measuring at least one additional miR gene product, wherein the miR is miR-155 and/or miR-152-prec;   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   bolstering the diagnosing of the subject as having, or at risk for developing, pancreatic 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 pancreatic cancer.   
     
     
         8 . The method of  claim 1 , further comprising:
 communicating the diagnosis to at least one person.   
     
     
         9 . The method of  claim 1 , wherein a miR signature of pancreatic cancer consists essentially of: miR-21, miR-17-5p, miR-191, miR-29b-2, miR-223, miR-128b, miR-199a-1, miR-24-1, miR-24-2, miR-146, miR-181b-1, miR-20a, miR-107, miR-32, miR-92-2, miR-214, miR-30c, miR-25, miR-221, and miR-106a. 
     
     
         10 . A method of inhibiting tumorigenesis in a subject who has pancreatic cancer, comprising:
 (1) determining the amount of at least one miR gene product in cancer cells from the subject, relative to control; and   (2) 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 miR-155 and/or miR-152-prec; 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: miR-103-2; miR-103-1; miR-24-2; miR-107; miR-100; miR-125b-2; miR-125b-1; miR-24-1; miR-191; miR-23a; miR-26a-1; miR-125a; miR-130a; miR-26b; miR-145; miR-221; miR-126; miR-16-2; miR-146; miR-214; miR-99b; miR-128b; miR-29b-2; miR-29a; miR-25; miR-16-1; miR-99a; miR-224; miR-30d; miR-92-2; miR-199a-1; miR-223; miR-29c; miR-30b; miR-129-1/2; miR-197; miR-17-5p; miR-30c; miR-7-1; miR-93-1; miR-140; miR-30a-5p; miR-132; miR-181b-1; miR-23b; miR-20a; miR-222; miR-27a; miR-92-1; miR-21; miR-129-1/2 prec; miR-150; miR-32; miR-106a; and miR-29b-1,
 such that tumorigenesis is inhibited in the subject. 
   
     
     
         11 . A method of identifying an inhibitor of tumorigenesis, comprising providing a test agent to a cell and measuring the level of at least one miR gene product associated with increased expression levels in pancreatic cancers, wherein a decrease in the level of the miR gene product in the cell, relative to a suitable control cell, is indicative of the test agent being an inhibitor of tumorigenesis.