Unraveling the oncogenic mechanisms of the lncRNA RMEL3 and its potential as therapeutic target

Abstract

Long non-coding RNAs (lncRNAs) constitute a large and diverse class of functional RNAs. We identified the lncRNA RMEL3 as an enriched transcript in melanoma, particularly in those carrying the BRAFV600E mutation and with a markedly invasive phenotype. The data indicate that RMEL3 functions as a positive regulator of the MAPK and PI3K pathways and a negative regulator of cell cycle inhibitory proteins, stimulating melanoma growth and protecting untransformed cells from cell cycle arrest and cell death caused by deprivation of growth factors and mitogens. In order to characterize its mechanism of action, we analyzed the interaction of the endogenous transcript with proteins. Among the identified candidates are proteins directly involved in the MAPK pathway (ARAF, FAM83D) and in the Hippo tumor suppressor pathway (STK3/MST2), among others, involved in DNA repair, transcriptional regulation, apoptosis, cytoskeleton, mRNA translation and energy metabolism. Combinations of ChIP-seq and RNAseq data from a wide variety of tissues reveal numerous regulatory elements near and within the gene and suggest a high complexity of transcript isoforms. Analysis of these data consolidates the notion that the canonical isoform (RMEL3_201) is highly restricted to melanoma, but the alternative isoform RMEL3_202 and, possibly, several other minor isoforms are expressed in different tissues, such as gonads, and embryonic, endothelial, adipose and neural cells. The two annotated isoforms and a circular one (hsa_circ_0142225) are expressed in melanoma and respond differently to treatment with a BRAFV600E inhibitor. Therefore, continuing the previous studies of our laboratory, we propose the following aims to be pursued in this project: i) identify and functionally characterize the complete transcripts of the RMEL3 gene expressed in different physiological, pathological and pharmacological contexts and investigate the repressive and activating mechanisms responsible for the specific expression pattern of each isoform; ii) validate the interactions of the RMEL3 transcript with the previously identified candidate proteins and analyze their impact on the MAPK, PI3K and Hippo signaling pathways in melanoma; iii) interfere with the expression of isoforms of the RMEL3 gene and perform phenotypic and functional complementation analyses, in vitro and in vivo. With this study, we seek to contribute to an accurate annotation of the RMEL3 gene and elucidation of the mechanisms by which the main transcript isoforms exert their functional activities. (AU)