Long Noncoding RNA Could Be Target for Melanoma Therapy Development

from Melanoma News Today – by Ines Martins –

Inhibition of a long noncoding RNA called RMEL3 may help treat melanoma patients, including those with a BRAF mutation, according to a recent study developed by researchers at the University of São Paulo in Brazil.

The study, “RMEL3, a novel BRAFV600E-associated long noncoding RNA, is required for MAPK and PI3K signaling in melanoma,” published in Oncotarget, shows that targeting RMEL3 can reduce the viability of cultured melanoma cell lines by up to 95 percent.

Long noncoding RNAs are molecules that do not contain information to generate a protein but participate in the regulation of gene expression, or in specific signaling pathways in the cell. RMEL3, one of the noncoding RNAs found in cells, is thought to participate in signaling pathways related to cell proliferation and survival.

“Our research suggests RMEL3 is expressed in most cases of melanoma. On the other hand, this RNA is rarely found in other kinds of tumor or even in healthy cells, so it’s a highly specific therapeutic and diagnostic target of considerable promise for development,” Enilza Espreafico, professor at the University of São Paulo’s Ribeirão Preto Medical School and principal investigator of the study, said in a press release.

Using databases with tumor sequencing projects, researchers identified 29 RNA sequences that were only expressed in melanoma cells. The team focused on three genes, RMEL1, RMEL2, and RMEL3, which were found to be expressed in tumor samples from patients and melanoma cell lines. RMEL3 was also found in skin lesions considered premalignant.

Using small RNA molecules that bind RMEL1-3 and induce their degradation, called interference RNA, the team found that RMEL3 inhibition induced the most intense reduction in melanoma cells’ viability.

The investigators silenced RMEL3 in five different cell lines — three with a BRAF mutation known to be associated with cancer, one without BRAF mutation, and one ovarian cancer cell line without the BRAF mutation but that functioned as a control because the cells do not express RMEL3.

“BRAF is the main proto-oncogene associated with the development of melanoma. Roughly 60 percent of cases of this type of cancer involve a mutation of BRAF, which codes for a kinase protein that initiates the MAPK signaling pathway, an important trigger of cell proliferation,” Espreafico said.

The researchers found that RMEL3 inhibition has the most dramatic effect in melanoma cell lines carrying the BRAF mutation. It reduces cell viability up to 95 percent. The melanoma cell line that lacked the BRAF mutation only had a 40 percent decrease in viability upon RMEL3 inhibition.

RMEL3 knockdown alters melanoma cell expression profile

long non coding RNA

A. TCGA patients were classified into two groups of RMEL3 expressions. RMEL3 Low group (n=105), constituted of patients with RMEL3 expression below 25th percentile and RMEL3 High group (n=117), constituted of patients with RMEL3 expressions above the 75th percentile of the total RMEL3 expression set*. Tukey’s box-and-whisker plot. B. Volcano plot and Heatmap C. displaying differentially expressed genes (log2 fold change <-2 or >2, adj. p-value <0.00001) between RMEL3 Low and High groups. D. A375-SM RMEL3 knockdown efficiency*. E. Canonical pathways enrichment of the validated genes by Ingenuity Pathway Analysis software. F. Cell-to-cell signaling and interaction network. Red squares are upregulated genes and green squares are downregulated after RMEL3 knockdown. White squares are connective molecules not differentially expressed. G. Pathways involvement of differentially expressed genes from TCGA analysis validated by RMEL3 knockdown. Green colored genes are downregulated after RMEL3 knockdown and red colored genes are upregulated. *Mann-Whitney test assigned p-value between columns individual comparisons.

Currently, researchers are examining the role of RMEL3 by inducing its artificial expression in both melanoma and healthy cells. In addition, they also aimed to access how frequently RMEL3 is expressed in melanoma patients by analyzing nearly 500 melanoma samples.

“We observed that RMEL3 was expressed to a greater or lesser extent in over 90 percent of the melanoma samples available. Together with the fact that it isn’t present in healthy tissue in the rest of the organism, this makes it a very interesting therapeutic target,” Espreafico said.

Source – Melanoma News Today

Goedert L, Pereira CG, Roszik J, Plaça JR, Cardoso C, Chen G, Deng W, Yennu-Nanda VG, Silva WA Jr, Davies MA, Espreafico EM. (2016) RMEL3, a novel BRAFV600E-associated long noncoding RNA, is required for MAPK and PI3K signaling in melanoma. Oncotarget [Epub ahead of print]. [article]

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