Transcription profiling of human ALL invitro models and patients to investigate glucocorticoid-regulated microRNAs and mirtrons in acute lymphoblastic leukemia

Glucocorticoids (GC) have a major impact on the biology of normal and malignant cells of the lymphoid lineage. This includes induction of apoptosis which is exploited in the therapy of acute lymphoblastic leukemia (ALL) and related lymphoid malignancies. MicroRNAs (miRNAs) and the related mirtrons are ~22 nucleotide RNA molecules implicated in the control of essential biological functions including proliferation, differentiation and apoptosis. They derive from polymerase-II transcripts but whether GCs regulate miRNA-encoding transcription units is not known. We investigated miRNA/mirtron expression and GC regulation in 8 ALL in vitro models and 13 ALL children undergoing systemic GC monotherapy using a combination of expression profiling techniques, real time RT-PCR and northern blotting to detect mature miRNAs and/or their precursors. We identified a number of GC-regulated miRNAs/mirtrons, including the myeloid-specific miR-223 and the apoptosis and cell cycle arrest-inducing mir15~16 cluster. Thus, the observed complex changes in miRNA/mirtron expression during GC treatment might contribute to the anti-leukemic GC effects in a cell context dependent manner. Experiment Overall Design: Glucocorticoid-sensitive T-ALL cell line CCRF-CEM-C7H2 was treated in 3 independent experiments either with 100nM dexametasone (a glucocorticoid) or 0.1% ethanol as an empty carrier control. Samples were taken at various timepoints (6 and 24 hours), RNA extracted and hybridized onto Affymetrix HGU133-plus2 microarrays. The microarray dataset was subsetted to probesets targetting potential primary microRNA transcripts (pri-miRNAs). Differentially expressed pri-miRNAs were identified for the comparisons of the 6h GC versus 6h EtOH (control) and for the 24h GC versus 24h EtOH (control) samples.