Multivariate Analysis Reveals a miRNA Profile Correlated To Karyotype and Outcome In Pediatric B-Cell Precursor ALL

Acute lymphoblastic leukemia (ALL) is the commonest childhood cancer and is characterized by the presence of recurring structural genetic alterations that have been associated to clinical response.Recently it has been shown that the deregulation of microRNAs (miRNA), a class of small RNAs that negatively control gene expression, is a common characteristic of hematological malignancies and may be related to the pathogenesis of leukemias. The aim of the current study was to explore which microRNAs are expressed by each subtype of pediatric B-cell precursor ALL and to determine their roles into clinical outcome. We analyzed samples from 94 children diagnosed as B-cell precursor ALL in Italy between 2000 and 2010 that were included in the AIEOP-BFM protocol of treatment. The patients were divided by cytogenetic subgroups of ALL. Cells CD34+ and CD19+ from healthy donors were used as negative controls. The miRNA signature was studied using microchips for miRNA microarray. We first performed a two-class comparison of miRNA expression between leukemic and non-leukemic samples and found 84 miRNAs differently expressed (P<0.01). A multivariate analysis of karyotype showed that 59 of these miRNAs were correlated to leukemia (P<0.01). All major subtypes of precursor B-cell ALL were analyzed: MLL-rearranged (10), TEL-AML1(15), E2A-PBX1(10), BCR-ABL(23), hyperdiploid(17), ‘normal Karyotype’ (19, defined as those not carrying the foregoing cytogenetic aberrations), and also the presence of IKAROS deletions was evaluated. Each subgroup was found to have unique microRNA-signature that differed from each other and from those of healthy hematopoietic cells. Both Kaplan Meier and Cox regression tests were performed to check how many of these miRNAs were correlated to clinic response, based on the induction failure, relapse, and survival. A multivariate analysis revealed that genetic subtypes and poor-responders patients display characteristic miRNA signatures. Specifically the mir-125b, 16-2, 24, 28-5p, 128a, 138-1 and 658 (all P<0.01) came out as independent prognostic factors predictive of event-free survival (EFS). IKAROS deletions did not come out as an independent prognostic factor, probably for being already associated to Ph+ and “BCR-ABL like” patients, who already have a poor prognosis. In addition, our group has previously shown that miR-125b may act as an oncogene and is correlated to a poor response in Ph+ samples, also increasing therapy resistance and leukemia aggressiveness in vivo. Further functional studies are needed to better explain the role of these miRNA and to provide new insights into the biology of pediatric ALL.