MicroRNA 15a and 16-1 Target Identification in Deletion 13 Multiple Myeloma

Deletion 13 multiple myeloma (MM) is detected in nearly 50 % of patients diagnosed with MM and confers a shorter survival. A region of minimal deletion was identified for chromosome 13 using Agilent 500K aCGH arrays that included microRNAs 15a and 16- 1. MicroRNAs (miRs) are small RNAs that negatively regulate gene expression through degradation of mRNA transcripts or translational inhibition. In order to determine the contribution of deletion of miRs 15a and 16-1 to MM progression, miR precursors were transfected into KMS-11 and JJN3 adherent myeloma cell lines and total RNA hybridized to Affymetrix U133 Plus 2.0 gene expression arrays for the purpose of identification of mRNA target transcripts. Thirty nanomolar miR 15a and 16-1 precursors and a nonsilencing siRNA control were transfected into adherent KMS-11 and JJN3 myeloma cell lines. Cultures were harvested 16 hours after transfection to minimize the downregulation of transcripts that are not direct targets of miRs 15a and 16-1. Total RNA was extracted using the miRNeasy kit to allow retention of the miR fraction for RT-PCR confirmation of miR over-expression following transfection. Following transfection of miR precursors, expression of miRs 15a and 16-1 were increased 64 and 128-fold, respectively, compared to non-silencing control. Total RNA was hybridized to Affymetrix gene expression arrays using protocols supplied by the manufacturer. Transcripts down-regulated following miR transfection were compared to mathematical models for prediction of miR targets. Additionally, the 3′ UTRs of down-regulated transcripts were inspected for complementarity to miR 15a and 16-1 seed sequences. RT-PCR validation of identified targets was performed. Cross reference of down-regulated transcripts with the TargetSCAN and PictarVERT miR prediction algorithms resulted in a list of 9 genes that represented potential miR-15a/16-1 targets in MM. This list included: FGF2, BCL2, CCNE1, V-MYB, WEE1, E2F7, CDK6, CDC25A and CDC27. Following target identification, reporter constructs were used to confirm direct regulation of transcripts by miRs 15a and 16-1. Functional investigation of miR targets was performed using siRNA reduction of identified targets followed by MTT assay and cell cycle analysis.