Scientists discovered two microRNAs — tiny RNA molecules that control the activity of several genes — playing a key role in the development of Friedreich’s ataxia (FA) that may be promising candidates for its treatment.
Their findings were reported in the study, “A Comprehensive Transcriptome Analysis Identifies FXN and BDNF as Novel Targets of miRNAs in Friedreich’s Ataxia Patients,” published in the journal Molecular Neurobiology.
FA is caused by the repetition of three nucleotides — the building blocks of DNA — specifically, one guanine (G) and two adenines (A), in the first intron of the frataxin (FXN) gene. An intron is an area of the gene that does not provide instructions to make a protein.
These nucleotide repeats prevent the FXN gene from making messenger RNA (mRNA) molecules that serve as templates for the production of frataxin, a small protein with a key role in iron metabolism, resulting in a severe decrease in its levels throughout the body.
Some studies have suggested that certain microRNAs (miRNAs) could play important roles in FA, including in the modulation of disease severity and some of its manifestations.
“As miRNAs can regulate the expression of a broad spectrum of genes, are used as biomarkers, and can serve as therapeutic tools, we decided to identify and characterize differentially expressed miRNAs [miRNAs produced at different levels] and their targets in [FA] cells,” investigators wrote.
To that end, a team from Poland and the U.S. used a powerful DNA sequencing technique called next-generation sequencing (NGS) to examine the RNA and miRNA profile of fibroblasts (skin cells) isolated from FA patients and healthy individuals (controls). NGS was used in 15 FA and 15 control cell lines.
After comparing the transcriptome of these cells, the investigators used bioinformatic analyses along with quantitative real-time polymerase chain reaction (qRT-PCR) to confirm their findings. Transcriptome refers to the group of all RNA molecules, or transcripts, produced from active genes in a cell or tissue; qRT-PCR is a technique to measure expression levels, or activity, of certain genes of interest.
From the 1,059 miRNAs identified, 13 were present at different levels in patient and control cell lines; five were higher levels in patient cells, and eight were higher in control cells.
Bioinformatic analyses indicated the FXN gene transcript was one of the targets of the five miRNAs produced at that higher level in patient-derived cells.
Additional experiments confirmed that one of these miRNAs, called miRNA-224-5p, targeted and silenced the FXN transcript, effectively lowering frataxin’s mRNA and protein levels.
“Uncovering miRNA(s) that efficiently target FXN mRNA could lead to the development of potential therapeutic interventions via blocking miRNA-mRNA interactions and consequently upregulating [increasing the activity of] FXN,” the researchers wrote.
They also found that miRNA-10a-5p — another miRNA found in high levels in patient cells — was able to bind and lower the levels of brain-derived neurotrophic factor (BDNF) transcript, a key modulator of nerve cell growth, maturation, and survival.
When the researchers used a gene-editing tool (called zinc-finger nuclease-mediated excision) to remove the excessive number of GAA repeats in the FXN gene of patient cells, they found the levels of miRNA-10a-5p significantly decreased, while those of BDNF were markedly increased.
“Combined with results of prior studies on the protective role of BDNF in neuronal degeneration in [FA] models, our study not only validated the miRNA-10a-5p-FXN–BDNF interplay, but also identified this miRNA as well as BDNF as potential therapeutic targets in [FA],” they wrote.
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