CHARACTERIZING THE ROLE OF LNCRNAS IN CONFERRING SENSITIVITY/RESISTANCE TO I-BET151 TREATMENT USING AN IN-VITRO MODEL OF LEUKEMIA CELL LINES

Abstract

Studies on mechanisms of drug resistance have extensively focused on protein-coding genes, yet cancer development and progression cannot be fully explained solely by the coding genome. Novel technologies revealed that only < 1% of the genome is protein-coding, with the non-coding genome harboring a crucial gene regulatory potential. Long non-coding RNAs (LncRNAs), which are RNA molecules greater than 200 nucleotides in length, have been presented as the main players of the non-coding genome along with their shorter microRNA (miRNA) counterparts, regulating gene expression at the transcriptional, post-transcriptional, translational, and epigenetic levels.

It has been shown that long intergenic non-coding RNA – Regulator of Reprogramming (LINC-ROR) and LINC01287 are implicated in several cancers with roles in resistance to drugs. LINC-ROR is responsive to the epigenetic drug inhibitor of bromodomain and extra-terminal proteins 151 (I-BET151) treatment at low concentrations in I-BET151-sensitive AML cell line (MV4-11) and LINC01287 was demonstrated to be differentially upregulated in I-BET151-resistant CML cell line (K562) relative to MV4-11. Here, we hypothesized that LINC-ROR and LINC01287 are the intrinsic I-BET151 sensitivity/resistance mediators of MV4-11 and K562 cell lines, respectively.

In our study, we explored LINC-ROR and LINC01287 expression profiles in cancer patients and blood cancer cell lines using publicly available cancer genome atlas (TCGA) and leukemia-lymphoma 100 (LL-100) panel datasets. We demonstrate their overexpression and uniqueness across several cancers and blood cancer cell lines of distinct cellular origins, lineages, and cancer subtypes. We also investigated in-silico lncRNA-miRNA interactions and discovered a unique role for LINC-ROR and LINC01287 in hematological malignancies through miRNA regulation. Lastly, following a fluorescently labeled siRNA-mediated gene knockdown approach coupled with cell sorting, we attempted to discover whether LINC-ROR knockdown recapitulates the effect of I-BET151 treatment on the MV4-11 cell line and if LINC01287 knockdown enhances the sensitivity of the K562 cell line to I-BET151. Interestingly, RT-qPCR on a panel of LINC01287 targets in K562 cells revealed promising trends. We further aimed to conduct RNA-sequencing but were limited with the logistics. Our findings if coupled with RNA-sequencing in the near future may provide greater support to our hypothesis and pave the way for further research on manipulating lncRNA-mediated epigenetic regulation in favor of disease treatment.