Microrna and use thereof in identification of b cell malignancies

Abstract

Disclosed are nucleic acid sequences, including microRNA sequences and cDNA sequences, as well as vectors, DNA libraries, microarrays, and recombinant cells comprising the nucleic acid sequences described herein. Methods of determining the B cell stage from which a B cell malignancy is derived. Methods of identifying B cell malignancies are also provided. Methods of diagnosing B cell malignancies are provided. Such methods comprise, in certain embodiments, detecting one or more microRNAs or cDNAs as disclosed herein.

1 . A composition comprising an isolated nucleic acid molecule having at least 80% sequence identity to any one of SEQ ID NOs: 763-1350 or 1565 or a complementary sequence thereof. 
     
     
         2 . The composition of  claim 1 , wherein the isolated nucleic acid molecule is a nucleic acid molecule having at least 90% sequence identity to any one of SEQ ID NOs: 763-1350 or 1565 or a complementary sequence thereof. 
     
     
         3 . (canceled) 
     
     
         4 . The composition of  claim 1 , wherein the isolated nucleic acid molecule is a nucleic acid molecule comprising any one of SEQ ID NOs: 763-1350 or 1565 or a complementary sequence thereof. 
     
     
         5 . The composition of  claim 1 , wherein the isolated nucleic acid molecule is a miRNA precursor molecule having the sequence of SEQ ID NOs: 763-1350 or 1565, or a DNA molecule coding the miRNA. 
     
     
         6 . The composition of  claim 1 , wherein the isolated nucleic acid molecule is either single-stranded or at least partially double-stranded. 
     
     
         7 . (canceled) 
     
     
         8 . The composition of  claim 1 , wherein the isolated nucleic acid molecule is selected from RNA or DNA molecules. 
     
     
         9 . The composition of  claim 1 , wherein the isolated nucleic acid molecule is a cDNA that corresponds to any one of SEQ ID NOs: 763-1350 or 1565. 
     
     
         10 . The composition of  claim 1 , wherein the isolated nucleic acid molecule comprises at least one modified nucleotide analog. 
     
     
         11 . The composition of  claim 1 , further comprising a carrier or vehicle, wherein the isolated nucleic acid molecule is suitable as a marker or modulator of a B cell malignancy, and wherein the carrier or vehicle is a pharmaceutically acceptable carrier or vehicle suitable for diagnostic or therapeutic applications. 
     
     
         12 - 14 . (canceled) 
     
     
         15 . The composition of  claim 1 , wherein the isolated nucleic acid molecule is operably linked to a recombinant expression vector. 
     
     
         16 . A cell comprising the recombinant expression vector of  claim 15 . 
     
     
         17 . (canceled) 
     
     
         18 . (canceled) 
     
     
         19 . A method of identifying a B cell malignancy in a subject comprising determining the level of expression of at least one microRNA in a sample comprising a B cell taken from the subject relative the level of expression of the at least one microRNA in a control sample, wherein the at least one microRNA is selected from the microRNAs listed in any one of Tables 4 and 7 to 35. 
     
     
         20 . (canceled) 
     
     
         21 . The method of  claim 19 , wherein the B cell malignancy is one of at least two potential B cell malignancies, wherein at least two of the potential B cell malignancies are derived from different B cell stages. 
     
     
         22 . (canceled) 
     
     
         23 . The method of  claim 19 , wherein the B cell malignancy is selected from chronic lymphocytic leukemia, follicular lymphoma, Hodgkin's lymphoma, activated B-cell diffuse large B cell lymphoma (DLBCL), germinal center-like DLBCL, and Burkitt lymphoma. 
     
     
         24 - 34 . (canceled) 
     
     
         35 . A kit comprising one or more sequences selected from a group consisting of
 (a) at least one primer sequence that can detect any one of SEQ ID NOs: 763-1350 or 1565, or a combination thereof;   (b) at least one isolated nucleic acid molecule having a sequence of any one of SEQ ID NOs: 1351-1564;   (c) the isolated nucleic acid molecule of  claim 1 ; and   (d) any combination of (a)-(c).   
     
     
         36 . (canceled) 
     
     
         37 . The kit of  claim 35 , wherein (a) further comprises enzymes and reagents that are adequate for performing an RT-PCR reaction. 
     
     
         38 - 41 . (canceled) 
     
     
         42 . The method of  claim 19 , further comprising determining whether the B cell malignancy in the sample is Burkitt lymphoma, activated B cell-like diffuse large B cell lymphoma (DLBCL), or germinal center-like DLBCL, comprising determining the level of expression of at least one microRNA in the sample relative to the level of expression of the at least one microRNA in the control sample, wherein the at least one microRNA is selected from the microRNAs listed in Table 7, column “GCBvsBL”; Table 7, column “GCBvsABC”; Table 8, column “ABCvsBL”; Table 10, column “BL miRNA list”; Table 10, column “GCB miRNA list”; Table 11; Table 14, column “BL High”; Table 14, column “ABC High”; Table 14, column “GCB High”; Table 32; or Table 35. 
     
     
         43 . The method of  claim 42 , comprising determining the level of expression of at least one microRNA selected from the microRNAs listed in Table 10, column “BL miRNA list”, and Table 14, column “BL High”; determining the level of expression of at least one microRNA selected from the microRNAs listed in Table 11 and Table 14, column “ABC High”; and determining the level of expression of at least one microRNA selected from the microRNAs listed in Table 10, column “GCB miRNA list”, and Table 14, column “GCB High”. 
     
     
         44 . The method of  claim 43 , wherein at least one microRNA is listed in only one column selected from the columns labeled “GCBvsBL” or “GCBvsABC” in Table 7 or “ABCvsBL” in Table 8. 
     
     
         45 . The method of  claim 42 , wherein at least one microRNA is listed in no more than two columns selected from the columns labeled “GCBvsBL” or “GCBvsABC” in Table 7 or “ABCvsBL” in Table 8.