Expression patterns of microRNAs associated with CML phases and their disease related targets

Machová Poláková et al. Molecular Cancer 2011, 10:41 http://www.molecular-cancer.com/content/10/1/41 RESEARCH Open Access Expression patterns of microRNAs associated with CML phases and their disease related targets Kateřina Machová Poláková1*, Tereza Lopotová1,2, Hana Klamová1, Pavel Burda3, Marek Trněný1, Tomáš Stopka3 and Jana Moravcová1 Abstract Background: MicroRNAs are important regulators of transcription in hematopoiesis. Their expression deregulations were described in association with pathogenesis of some hematological malignancies. This study provides integrated microRNA expression profiling at different phases of chronic myeloid leukemia (CML) with the aim to identify microRNAs associated with CML pathogenesis. The functions of in silico filtered targets are in this report annotated and discussed in relation to CML pathogenesis. Results: Using microarrays we identified differential expression profiles of 49 miRNAs in CML patients at diagnosis, in hematological relapse, therapy failure, blast crisis and major molecular response. The expression deregulation of miR-150, miR-20a, miR-17, miR-19a, miR-103, miR-144, miR-155, miR-181a, miR-221 and miR-222 in CML was confirmed by real-time quantitative PCR. In silico analyses identified targeted genes of these miRNAs encoding proteins that are involved in cell cycle and growth regulation as well as several key signaling pathways such as of mitogen activated kinase-like protein (MAPK), epidermal growth factor receptor (EGFR, ERBB), transforming growth factor beta (TGFB1) and tumor protein p53 that are all related to CML. Decreased levels of miR-150 were detected in patients at diagnosis, in blast crisis and 67% of hematological relapses and showed significant negative correlation with miR-150 proved target MYB and with BCR-ABL transcript level. Conclusions: This study uncovers microRNAs that are potentially involved in CML and the annotated functions of in silico filtered targets of selected miRNAs outline mechanisms whereby microRNAs may be involved in CML pathogenesis. Introduction Mammalian microRNAs (miRNA, miR) are short noncoding RNAs that regulate preferentially gene expression by inhibiting translation of specific target mRNAs. MiRNA-mRNA matching is based on imperfect sequence base-pairing with the required complementarity centered over positions 2 - 8 of mRNA’s seed sequence [1]. Depending on specific target genes, miRNAs regulate many cellular functions such as developmental timing, signal transduction, apoptosis, cell proliferation and tumorigenesis [2-5]. Thus, gene expression and role of miRNAs are currently being largely studied in human malignancies and chemical compounds that regulate miRNA levels are potentially very * Correspondence: 1 Institute of Hematology and Blood Transfusion, Prague, U Nemocnice 1, 128 20, Czech Republic Full list of author information is available at the end of the article important for developing new treatment strategies in chronic myeloid leukemia (CML). The first miRNA molecules that have been associated with human leukemia pathogenesis were found in chronic lymphocytic leukemia (CLL) [6]. MiR-15 and miR-16 are located in a genomic region that is frequently deleted in CLL, thus the expression of these two miRNAs is downregulated. Other works brought the evidence that many miRNAs are indeed found at chromosomal breakpoints and genomic regions associated with cancer [7,8]. In CML the following miRNAs were associated with the disease pathogenesis. For instance, the miR-203 was found to be epigenetically silenced in human leukemic Philadelphia chromosome-positive (Ph+) cell lines; this is in line with the observation that BCR-ABL and ABL kinases are miR-203 putative targets [9]. Derivative 9q+ chromosome deletions carrying miR-199b that occurred in some CML patients were associated with miR-199b © 2011 Poláková et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Machová Poláková et al. Molecular Cancer 2011, 10:41 http://www.molecular-cancer.com/content/10/1/41 decrease [10]. Venturini et al. [11] showed miR-17-92 cluster (onkomir-1) to be aberrantly expressed in CD34 + cells of CML patients. Agirre at al. [12] analyzed the expression of 157 miRNAs in mononuclear and CD34+ cells separated from bone marrow of 6 CML patients at diagnosis and found 11 miRNAs (e.g. miR-150, miR151, miR-221, miR-127, miR-16) aberrantly expressed in CD34+ cells and 53 miRNAs differentially expressed in mononuclear cells (e.g. miR-150, miR-126, miR-221, miR-222, miR-21). Two recent works contributed to the knowledge about expression change in specific microRNAs associated with resistance to imatinib or responsiveness to imatinib after the treatment initiation in CML patients [13,14]. A group of 19 miRNAs (e.g. miR191, miR-29a, miR-422b, miR-100, miR-326, miR-26a) were identified as possible predictors for clinical resistance to imatinib in patients with newly diagnosed CML [13]. A relatively rapid increase in the expression of miR-150 and miR-146a and decrease of miR-142-3p and miR-199b-5p in peripheral blood mononuclear cells (PBMCs) of patients newly diagnosed with CML was found two weeks after imatinib initiation [14]. In this study, we used an array platform to characterize differentially expressed miRNAs in peripheral blood total leukocytes of patients at different stages of CML including diagnosis, major molecular response, therapy failure, hematological relapse, accelerated phase and blast crisis with the aim to identify microRNAs associated with pathogenesis of CML. To the best of our knowledge, such integrated microRNA profiling during the course of CML has not yet been performed. Hierarchical clustering analysis based on expression profiles of 49 miRNAs clearly separated patients at diagnosis, hematological relapse and blast crisis from those in major molecular response and therapy failure. We used in silico analyses to better understand the targets of 17 selected miRNAs whose deregulation was confirmed by real-time quantitative PCR (RT-qPCR). Based on our previous results demonstrating that miR-150 downregulation is associated with CML [15], we further validated miR-150 expression in a larger number of patients (n = 70). As MYB represents functionally validated target of miR-150 [16], its gene expression analysis was performed on the same patient cohort. Our data provide significant inverse correlations between miR-150 and MYB expression and BCR-ABL transcript level and indicate that this relationship is potentially important for pathogenesis in CML. Materials and methods Patient samples Twenty four patient samples of total leukocytes from peripheral blood (Table 1) were used to prepare pools representing different CML ph (...truncated)