DIAGNOSIS AND TREATMENT OF CANCERS WITH MicroRNA LOCATED IN OR NEAR CANCER ASSOCIATED CHROMOSOMAL FEATURES

Abstract

MicroRNA genes are highly associated with chromosomal features involved in the etiology of different cancers. The perturbations in the genomic structure or chromosomal architecture of a cell caused by these cancer-associated chromosomal features can affect the expression of the miR gene(s) located in close proximity to that chromosomal feature. Evaluation of miR gene expression can therefore be used to indicate the presence of a cancer-causing chromosomal lesion in a subject. As the change in miR gene expression level caused by a cancer-associated chromosomal feature may also contribute to cancerigenesis, a given cancer can be treated by restoring the level of miR gene expression to normal. microRNA expression profiling can be used to diagnose cancer and predict whether a particular cancer is associated with an adverse prognosis. The identification of specific mutations associated with genomic regions that harbor miR genes in CLL patients provides a means for diagnosing CLL and possibly other cancers.

1 . A method of determining increased risk of a human subject developing B-cell chronic lymphocytic leukemia (CLL) or increased likelihood of the presence of CLL in a human subject comprising the steps of:
 (i) measuring in a blood sample from the subject the level of one or more microRNAs selected from the group consisting of miR-029a microRNA, miR-029b-2 microRNA and miR-029c microRNA; and   (ii) comparing the level of the one or more microRNAs in the sample to a control level of the one or more microRNAs,   
       wherein an increase in the level of the one or more microRNAs in the sample relative to the control level of the one or more microRNAs is indicative of the subject either having increased risk of developing CLL or increased likelihood of the presence of CLL. 
     
     
         2 . The method of  claim 1 , wherein the level of the one or more microRNAs in the sample is measured using an assay selected from the group consisting of northern blot analysis, in situ hybridization and quantitative reverse transcriptase polymerase chain reaction. 
     
     
         3 . The method of  claim 1 , wherein the subject has an unmutated IgV H  gene, positive ZAP-70 expression, or a combination thereof. 
     
     
         4 . The method of  claim 1 , wherein the miR-029a microRNA comprises SEQ ID NO:67 or SEQ ID NO:68. 
     
     
         5 . The method of  claim 1 , wherein the miR-029a microRNA comprises nucleotides 41-62 of SEQ ID NO:68. 
     
     
         6 . The method of  claim 1 , wherein the miR-029b-2 microRNA comprises SEQ ID NO:251. 
     
     
         7 . The method of  claim 1 , wherein the miR-029b-2 microRNA comprises nucleotides 51-70 of SEQ ID NO:251. 
     
     
         8 . The method of  claim 1 , wherein the miR-029c microRNA comprises SEQ ID NO:69. 
     
     
         9 . The method of  claim 1 , wherein the miR-029c microRNA comprises nucleotides 64-85 of SEQ ID NO:69. 
     
     
         10 . A method of determining increased risk of a human subject developing B-cell chronic lymphocytic leukemia (CLL) or increased likelihood of the presence of CLL in a human subject comprising the steps of:
 (1) reverse transcribing one or more microRNAs selected from the group consisting of miR-029a microRNA, miR-029b-2 microRNA and miR-029c microRNA from a blood sample from the subject to provide at least one target oligodeoxynucleotide for each of the one or more microRNAs;   (2) hybridizing the at least one target oligodeoxynucleotide for each of the one or more microRNAs to a microarray comprising miRNA-specific probe oligonucleotides that include at least one microRNA-specific probe oligonucleotide for each of the one or more microRNAs to provide a hybridization profile for the sample, wherein the hybridization profile includes a hybridization signal for each of the one or more microRNAs; and   (3) comparing the sample hybridization profile to a control hybridization profile, wherein the control hybridization profile includes a control hybridization signal for each of the one or more microRNAs,   wherein a hybridization signal of the one or more microRNAs in the sample hybridization profile that is greater than the control hybridization signal for the microRNA in the control hybridization profile indicates the subject has increased risk of developing CLL or increased likelihood of the presence of CLL.   
     
     
         11 . The method of  claim 10 , wherein the microarray comprises miRNA-specific probes oligonucleotides for a substantial portion of the human miRNome. 
     
     
         12 . The method of  claim 10 , wherein the subject has an unmutated IgV H  gene, positive ZAP-70 expression, or a combination thereof. 
     
     
         13 . A method of determining increased risk of a human subject developing B-cell chronic lymphocytic leukemia (CLL) associated with one or more adverse prognostic markers or increased likelihood of the presence of CLL associated with one or more adverse prognostic markers in a human subject comprising the steps of:
 (1) reverse transcribing one or more microRNAs selected from the group consisting of miR-029a microRNA, miR-029b-2 microRNA and miR-029c microRNA from a blood sample from the subject to provide at least one target oligodeoxynucleotide for each of the one or more microRNAs;   (2) hybridizing the at least one target oligodeoxynucleotide for each of the one or more microRNAs to a microarray comprising miRNA-specific probe oligonucleotides that include at least one microRNA-specific probe oligonucleotide for each of the one or more microRNAs to provide a hybridization profile for the sample, wherein the hybridization profile includes a hybridization signal for each of the one or more microRNAs; and   (3) comparing the sample hybridization profile to a control hybridization profile, wherein the control hybridization profile includes a control hybridization signal for each of the one or more microRNAs,   wherein a hybridization signal of the one or more microRNAs in the sample hybridization profile that is greater than the control hybridization signal for the microRNA in the control hybridization profile indicates the subject has increased risk of developing CLL associated with one or more adverse prognostic markers or increased likelihood of the presence of CLL associated with one or more adverse prognostic markers.   
     
     
         14 . The method of  claim 13 , wherein the one or more adverse prognostic markers are selected from the group consisting of: positive ZAP-70 expression; and an unmutated IgV H  gene; or a combination thereof. 
     
     
         15 . The method of  claim 13 , wherein the subject has an unmutated IgV H  gene, positive ZAP-70 expression, or a combination thereof.