Comparative RNA-seq analyses identify new microRNA biomarkers and candidate target genes in patients’ drug-resistant CD34+ CML stem/progenitor cells

Therapeutic targeting of BCR-ABL by ABL tyrosine kinase inhibitors (TKIs) has led to a significant survival benefit for early phase CML patients. However, TKI monotherapies are rarely curative; with persistence of leukemic stem cells, emergence of resistance and relapses remaining as challenges. To identify miRNAs in TKI-insensitive CD34+ stem/progenitor cells that might serve as potential biomarkers and/or therapeutic targets, we used Illumina sequencing to create absolute miRNA expression profiles from treatment-naïve CD34+ cells obtained at diagnosis from TKI-responders and nonresponders, and normal bone marrow (NBM) as controls. DESeq analysis revealed 63 differentially expressed miRNAs between CML and NBM samples (P<0.05); and 12 between TKI-responders and nonresponders. 34 novel miRNAs were also identified in CD34+ CML cells. 32 of the 63 differentially expressed miRNAs were confirmed in CD34+ cells from IM-responders (n=12), nonresponders (n=10) and normal individuals (n=11). Importantly, significant changes in some of these miRNAs were detected in CD34+ cells from CML patients (n=60) after 3-month nilotinib (NL) treatment; 18 normalized after NL therapy, whereas 10 showed little change. We also identified 1,210 differently expressed mRNAs that are predicted targets of the deregulated miRNAs, by comparing RNA-seq data from the same CML and NBM samples. Strikingly, only 7 differentially expressed mRNAs were predicted targets of the deregulated miRNAs when comparing TKI-responders and nonresponders. These miRNAs and their target genes may serve as useful biomarkers to predict clinical response of patients to TKIs and may point to novel therapeutic targets.