Discovery of new microRNAs by small RNAome deep sequencing in childhood acute lymphoblastic leukemia

We hypothesized that many miRNAs relevant to acute lymphoblastic leukemia (ALL) in children are unknown. In order to discover these miRNAs we applied high-throughput sequencing to pooled fractions of leukemic cells obtained from 89 pediatric patients covering seven well-defined genetic types of ALL and normal hematopoietic tissues. This method led to the identification of in total 78 million small RNA reads representing 554 known, 28 novel and 397 candidate novel miR-genes. Of these 154 known, 10 novel and 170 candidate novel miRNAs were only expressed in ALL but not in normal hematopoietic cells, whereas 141 known, 2 novel and 82 candidate novel miRNAs were unique to normal hematopoietic cells. Real-time quantitative PCR analyses confirmed the aberrant expression of mature miRNAs in different ALL types which may suggest their importance to the underlying biology of ALL. Novel sol-miR-23 was undetectable in precursor B-ALL but was expressed in normal bone marrow and CD34-positive cells and was associated with an upregulation of its predicted target oncogene SOX4 (P<0.0001). The identification of more than 1000 miR-genes being differentially expressed in leukemic subtypes and normal hematopoietic cells forms a comprehensive repository for further functional studies to understand the role of miRNAs in the biology of different types of ALL.