Deciphering the cross-talking of human competitive endogenous RNAs in K562 chronic myelogenous leukemia cell line

Abstract

Chronic myelogenous leukemia (CML) is a myeloproliferative disorder characterized by increased proliferation or abnormal accumulation of granulocytic cell line without the depletion of their capacity to differentiate. A reciprocal chromosomal translocation proceeding to the 'Philadelphia chromosome', involving the ABL proto-oncogene and BCR gene residing on Chromosome 9 and 22 respectively, is observed to be attributed to CML pathogenesis. Recent studies have been unraveling the crucial role of genomic 'dark matter' or the non-coding repertoire in cancer initiation and progression. The intricate cross-talk between competitive endogenous RNAs (ceRNAs) provides a scaffold to systematically functionalize the miRNA response element harboring non-coding RNAs and incorporate them with the protein-coding RNA dimension in complex ceRNA networks. This network of coding and non-coding transcriptome linked by shared miRNAs evidently offers a platform to elucidate the complex regulatory interactions at the post-transcriptional level in human cancers. In this context, analyzing CML, from the perspective of the ceRNA hypothesis, surely craves intensive attention and a comprehensive discussion. Here, we performed RNA-seq data analysis to retrieve Lymphoblastoid and CML coding as well as non-coding repertoire and constructed a ceRNA network for the CML cell line, considering the non-cancer lymphoblastoid cell line as the control. We investigated if any alteration exists in the ceRNA landscape of the transcripts which are exhibiting differential expression across the two cell lines and observed that the major ceRNA regulators vary in cancer network when compared with the Lymphoblastoid network. The top ranked significant functional modules in the ceRNA network display cancer associated attributes and reveal putative regulators in CML pathogenesis.

Identifying Dysregulated lncRNA-Associated ceRNA Network Biomarkers in CML Based on Dynamical Network Biomarkers

“…He et al found that SNHG5 promoted imatinib resistance in CML via acting as a ceRNA against miR-205-5p [7]. Sen et al constructed a ceRNA network for the CML cell line, and the top ranked significant functional modules in the ceRNA network displayed cancer associated attributes and revealed putative regulators in CML pathogenesis [8].…”

Comprehensive evaluation of differential lncRNA and gene expression in patients with intervertebral disc degeneration

“…Additionally, competing endogenous RNAs (ceRNAs) participate in microRNA (miRNA)-dependent crosstalk and contribute to the complexity of gene regulation, and may aid in the understanding of disease pathobiology ( 9 ). lncRNAs regulate the expression of neighboring coding genes through various mechanisms and may function as ceRNAs to modulate the derepression of miRNA targets ( 10 ). In recent years, the roles of lncRNAs in several diseases and cancers have been investigated ( 11 , 12 ).…”