In Silico Analysis of miR-223 and miR-181b and Their Target Genes in the Pathogenesis of Acute Promyelocytic Leukaemia

Abstract

Acute promyelocytic leukaemia (APL) is the M3 subtype of acute myeloid leukaemia (AML). The hallmark for APL diagnosis is the reciprocal chromosomal translocation between chromosome 15 and 17 to produce the PML/RARα fusion gene [1]. The combination treatment of all-trans retinoic acid and arsenic trioxide (ATRA- ATO) is 97% effective in treating APL, however the molecular mechanism of the pathogenesis of APL is yet to be understood. The discovery of miRNAs and epigenetics as potential prognostic biomarkers and therapeutic targets in various cancers including APL must be further explored. miR-223 downregulation in APL was widely shown to be associated with worse prognosis in previous studies [2]; while miR-181b upregulation in APL was shown to be associated with worse prognosis in previous studies, although the findings varied based on the ethnic populations that were involved in the studies [3].
 
 In order to understand more about the roles of these miRNAs, this study was conducted with the objective to investigate the roles of targeted genes regulated by mir-223 and mir-181b in APL and other cancers, as well as the signaling pathways involving these miRNAs in the pathogenesis of APL and other cancers. In silico analysis was conducted using miRDB 6.0 database to identify the target genes of miR-223 and miR-181b and filter them to relevance and significant expression in APL cell lines NB4 and HL60. Only the target genes with a target score of 80 or higher, and target expression of 20 RPKM or higher, with confirmation by experimentally validated articles were included.
 
 In silico analysis of miR-223 revealed 162 target genes, while 612 target genes were regulated by miR-181b. The validated target genes were then obtained by comparing the predicted target genes to experimentally validated articles. 116 of the target genes of miR-223 were found to be relevant in cancers in experimentally validated articles, whereas 156 of the target genes of miR-181b were found to be relevant in cancers in experimentally validated articles. The 14 target genes of miR-223 relevant in APL cell lines with expression level more than 20 RPKM and supported by experimentally validated articles include NXT1, ACSL4, LRRFIP1, NOP2, DENR, AIMP1, DEK, LRRC59, YWHAQ, XRCC5, LAMP2, RAB14, ARF6, and ATP6V1B2. On the other hand, the 15 target genes of miR-181b relevant in APL cell lines with expression level more than 20 RPKM and supported by experimentally validated articles include DDX3X, TNPO1, DMXL2, ARF6, ZFP36L2, PTBP3, SCD, GIGYF1, SLC25A37, PNRC2, TCERG1, RBBP7, WDR82, PRKCD, and ACSL4.
 
 GeneCodis 4 database was used for pathway analysis, which identified 159 KEGG signaling pathways involving the target genes of miR-223 and 203 KEGG signaling pathways involving the target genes of miR-181b (Table 1 and Table 2). There were 13 KEGG signaling pathways involving the target genes of miR-223 which were most significant pertaining to APL and other cancers. Meanwhile, there were 14 KEGG signaling pathways involving the target genes of miR-181b which were most significant pertaining to APL and other cancers.
 It can be concluded from this study that miR-223 and miR-181b play important roles in the pathogenesis of APL through the regulation of gene expression and activation of signaling pathways. Nevertheless, the functional roles of miR-223 and miR-181b in APL need to be further investigated through experimental validation by in vitro study using APL cell lines to further aid in the discovery of novel prognostic biomarkers and potential therapeutic targets of APL.