MicroRNA Expression Signature for Predicting Survival and Metastases in Hepatocellular Carcinoma

Abstract

Provided herein are microarrays, kits, methods and compositions for the diagnosis, prognosis and treatment of Hepatocellular carcinoma (HCC). Also provided are methods of identifying anti-HCC agents.

1 . An array, comprising: one or more miRNA probes immobilized on a solid support, each probe comprising:
 an miRNA coding sequence of one of SEQ ID NOs:1-22 (miR-126, miR-122, miR-148b, miR-124a, miR-194, miR-30c, miR-30a, miR-148a, miR-30e, miR-34a, let-7g, miR-125b, miR-1, miR-19a, miR-15a, miR-9, miR-185, miR-207, miR-219-5p, miR-219-3p, miR338-5p, miR-338-3p; and   an amine attached to the 5′ or 3′ end of the probe.   
     
     
         2 . An array, comprising one or more miRNA probes immobilized on a solid support, each probe comprising:
 an miRNA coding sequence of one or more of: miR-30c [SEQ ID NO: 6], mir-124A [SEQ ID NO: 4], miR-207 [SEQ ID NO: 18] and miR-219 [SEQ ID NO: 20] and combinations thereof; and   an amine attached to the 5′ or 3′ end of the probe,   
     
     
         3 . The array of  claim 1 , wherein the miRNA array comprises miRNA probes having miRNA coding sequence that includes the entire processed miRNA sequence. 
     
     
         4 . The array of  claim 3 , wherein the miRNA coding sequence also includes at least 2-5 nucleotides of coding sequence upstream and/or downstream of the processed miRNA sequence. 
     
     
         5 . The array of  claim 4 , wherein the miRNA coding sequence includes 4 nucleotides of coding sequence upstream and downstream of the processed miRNA sequence. 
     
     
         6 . The array of  claim 4 , wherein each probe further comprises: c) at least a first linker sequence flanking the miRNA coding sequence. 
     
     
         7 . A kit for generating a miRNA profile for a test sample comprising, in suitable container means, two or more miRNA probes wherein the probes have one or more miRNA coding sequences of SEQ ID NOs: 1-22. 
     
     
         8 . The kit of  claim 7 , further comprising reagents for labeling miRNA in the sample. 
     
     
         9 . A kit for generating a miRNA profile for a test sample comprising, in suitable container means, two or more miRNA probes wherein the probes have one or more miRNA coding sequences of: miR-30c [SEQ ID NO: 6], mir-124A [SEQ ID NO: 4], miR-207 [SEQ ID NO: 18] and miR-219 [SEQ ID NO: 20] and combinations thereof. 
     
     
         10 . The kit of  claim 10 , further comprising reagents for labeling miRNA in the sample. 
     
     
         11 . A collection of detection probes able to specifically hybridize to at least one RNA selected from the group comprising: miR-30c [SEQ ID NO: 6], mir-124A [SEQ ID NO: 4], miR-207 [SEQ ID NO: 18] and miR-219 [SEQ ID NO: 20]. 
     
     
         12 . A method of identifying an anti-hepatocellular carcinoma (HCC) test agent, comprising:
 a) contacting a HCC cell with a test agent; and   b) measuring the level of at least one miR gene product selected from one or more of SEQ ID NOs. 1-22, an alteration in the level of the miR gene product in the HCC cell, relative to a suitable control HCC cell, being indicative of the test agent being an anti-HCC agent.   
     
     
         13 . The method of  claim 12 , wherein the miR gene product comprises: miR-30c [SEQ ID NO: 6], mir-124A [SEQ ID NO: 4], miR-207 [SEQ ID NO: 18] and/or miR-219 [SEQ ID NO: 20]. 
     
     
         14 . A method to identify a human who has a poor survival prognosis for hepatocellular carcinoma (HCC), comprising:
 a) obtaining a miR-containing sample from a human;   b) conducting laboratory analysis of the sample so as to obtain physical data whether the sample includes an alteration in at least one of the levels of miR-219, miR-207, miR-30c and/or miR-124a; and   c) identifying the human as one who has a poor prognosis for HCC if the physical data indicate that the sample comprises an alteration of at least one of the levels of miR219 and miR-207 that are above the control levels, and/or of at least one of the levels of miR-30c and miR-124a that are below control levels.   
     
     
         15 . The method of  claim 14 , wherein the step c) distinguishes HCC venous metastasis from metastasis-free HCC. 
     
     
         16 . The method of  claim 14 , wherein the step c) predicts survival and recurrence of HCC patients with multinodular or solitary tumors. 
     
     
         17 . The method of  claim 14 , further including conveying results obtained from the laboratory analysis to the human. 
     
     
         18 . The method of  claim 14 , wherein the laboratory analysis of miR-containing sample is measured using Northern blot analysis.