Differential expression of miRNAs in acute myeloid leukemia quantified by Nextgen sequencing of whole blood samples

Abstract

New approaches are needed for understanding and treating acute myeloid leukemia (AML). MicroRNAs (miRs) are important regulators of gene expression in all cells and disruption of their normal expression can lead to changes in phenotype of a cell, in particular the emergence of a leukemic clone. We collected peripheral blood samples from 10 adult patients with newly diagnosed AML, prior to induction chemotherapy, and 9 controls. Two and a half ml of whole blood was collected in Paxgene RNA tubes. MiRNA was purified using RNeasy mini column (Qiagen). We sequenced approximately 1000 miRs from each of 10 AML patients and 9 controls. In subset analysis, patients with NPM1 and FLT3 mutations showed the greatest number of miRNAs (63) with expression levels that differed from control with adjusted p-value of 0.05 or less. Some of these miRs have been described previously in association with leukemia, but many are new. Our approach of global sequencing of miRs as opposed to microarray analysis removes the bias regarding which miRs to assay and has demonstrated discovery of new associations of miRs with AML. Another strength of our approach is that sequencing miRs is specific for the 5p or 3p strand of the gene, greatly narrowing the proposed target genes to study further. Our study provides new information about the molecular changes that lead to evolution of the leukemic clone and offers new possibilities for monitoring relapse and developing new treatment strategies.

Assessment of the Diagnostic Potential of miR-29a-3p and miR-92a-3p as Circulatory Biomarkers in Acute Myeloid Leukemia

“…Such relationship is considered a hotspot for research, which motivated many groups to work on expression profiling of miRNAs in different cellular contexts and in different types of neoplasms (Peng and Croce, 2016;Liao et al, 2017;He et al, 2019). Interestingly, each type of leukemia had unique profile of expressed microRNA linked with specific translocation or genetic mutations (Zhang et al, 2009), and such patterns highlighted the potential to use such profiling strategy to discriminate between subtypes of leukemias as well as to predict disease progression (Chan et al, 2011;Pandita et al, 2019). Genes responsible for the production of miRNAs are first transcribed into hairpin structured precursor microRNA molecules, which then are processed to give rise into the mature miRNAs; 19-22-nt long (Bartel, 2004).…”

Regulatory Innate Lymphoid Cells: A new subset of innate immune lymphocytes with more potential functions to be discovered in immune regulation

“…15,16,17 Some studies have demonstrated that certain miRNAs play an important role in certain malignant diseases such as AML with NPM1+/FLT3+ mutations. 18 One of the miRNAs associated with NPM1+/FLT3+ AML, miR-10a-5p showed the most statistically significant adjusted pvalue in the yield as well as the highest fold change. This miRNA had been described in patients with NPM1 mutations.…”

Expression, Regulation and Function of microRNA as Important Players in the Transition of MDS to Secondary AML and Their Cross Talk to RNA-Binding Proteins

“…Comparison of qPCR and microarray technology with deep sequencing results using the Illumina platform demonstrated the best correlation between the Agilent qPCR platform and the deep sequencing [ 76 , 77 ]. A recent study of global miRNA sequencing in AML samples showed an advantage to microarray analysis, since it removes the bias due to its specificity regarding the 5p or 3p strand of the gene that might have functional relevance [ 78 ]. These technologies have been extended to single cell RNA sequencing.…”