Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs

Abstract

A role for microRNA (miRNA) has been recognized in nearly every biologic system examined thus far. A complete delineation of their role must be preceded by the identification of all miRNAs present in any system. We elucidated the complete small RNA transcriptome of normal and malignant B cells through deep sequencing of 31 normal and malignant human B-cell samples that comprise the spectrum of B-cell differentiation and common malignant phenotypes. We identified the expression of 333 known miRNAs, which is more than twice the number previously recognized in any tissue type. We further identified the expression of 286 candidate novel miRNAs in normal and malignant B cells. These miRNAs were validated at a high rate (92%) using quantitative polymerase chain reaction, and we demonstrated their application in the distinction of clinically relevant subgroups of lymphoma. We further demonstrated that a novel miRNA cluster, previously annotated as a hypothetical gene LOC100130622, contains 6 novel miRNAs that regulate the transforming growth factor-␤ pathway. Thus, our work suggests that more than a third of the miRNAs present in most cellular types are currently unknown and that these miRNAs may regulate important cellular functions. (Blood. 2010;116(23):e118-e127)

MicroRNAs as prognostic markers in indolent primary cutaneous B-cell lymphoma

“…18,20 These miRNAs were selected according to the evidence regarding its association with particular stages of B-cell differentiation. We used commercial (Taqman) probes against miR-150, miR-155, miR-331, miR-221, miR-222, miR-223, miR-15a, miR-16, miR-17, miR-19a and miR-93.…”

“…17 Over 700 miRNAs have been verified in humans, although recent studies have identified over 1000 miRNA species in human B cells. 18 Various miRNAs are associated with particular normal B-cell differentiation stages. [18][19][20] For example, miR-150 was first found to be expressed in mature B cells and to regulate B-cell differentiation by targeting the transcription factor c-Myb.…”

“…18 Various miRNAs are associated with particular normal B-cell differentiation stages. [18][19][20] For example, miR-150 was first found to be expressed in mature B cells and to regulate B-cell differentiation by targeting the transcription factor c-Myb. 21 miR-223 is overexpressed in naive and memory cells relative to germinal center cells.…”

“…The expression of miR-223 in the naive stage was found to inhibit the expression of transcription factors, such as LMO2, that are expressed at high levels in non-neoplastic germinal center B cells. 20 Other miRNAs are known to be overexpressed in the germinal center stage of differentiation, compared with either naive or memory B cells, 18 including miR-17-5p and miR-155. Many of these miRNAs have been found to be deregulated in the neoplastic counterparts of these B cells.…”

“…[22][23][24] This study aimed to characterize the miRNA expression profile of a series of primary cutaneous B-cell lymphomas. On the basis of published data, 18,20,25 we selected a set of 11 miRNAs known to be associated with a particular normal B-cell stage of differentiation. We evaluated their expression by RT-PCR in a cohort of 68 primary cutaneous B-cell lymphoma patients with formalin-fixed, paraffin embedded tissue available from the diagnostic sample.…”