New studies have found the mechanisms behind RNA cluster formation inside brain cells. This finding is particularly important to the study of neurodegenerative diseases such as Huntington’s disease and amyotrophic lateral sclerosis (ALS). Tharun Selvam Mahendran is the lead on this impactful study under the guidance of Priya Banerjee. As a team, they find out how toxic aggregates fall apart, revealing new therapeutic avenues for diseases that do not have good treatments today.
RNA clusters condense when RNA assorted with proteins and, for certain clusters, DNA. The issues with these clusters seem to concentrate within cells that are at risk from neurodegenerative diseases. The researchers found that these clusters require a particular setting for seeding and accumulating to take place and develop. It’s this process that’s dictated by structures known as biomolecular condensates. Inside these condensates, multi-component interactions further promote RNA aggregation and the formation of solid-like clusters.
Understanding RNA Clusters
The formation of these RNA clusters is not a stochastic process, but directed by the cellular microenvironment. The research shows that repeat RNAs are inherently sticky, but they don’t clump up on their own. Rather, they must be under the right circumstances to extend from their compact three-dimensional forms and aggregate.
“Repeat RNAs are inherently sticky, but interestingly, they don’t stick to each other just by themselves because they fold into stable 3D structures. They need the right environment to unfold and clump together, and the condensates provide that,” – Tharun Selvam Mahendran.
In addition to this breakthrough, the researchers noticed that even after the host biomolecular condensate had dissolved, the RNA clusters were still visible. This implies that even though the collective environment can be modulated to shift overall conditions, the underlying permissive mechanisms enabling RNA aggregation are still quite resilient and robust.
“Crucially, we also found that the solid-like repeat RNA clusters persist even after the host condensate dissolves,” – Tharun Selvam Mahendran.
Preventing Cluster Formation
To thwart these damaging impacts of RNA aggregation, the collaborative research team implemented their experimental plan. They found a possible way forward, honing in on an RNA-binding protein called G3BP1. This protein is normally found in most cells and it has an important function in preventing the reappeared RNA from clustering together.
“The RNA clusters come about from the RNA strands sticking together, but if you introduce another sticky element into the [condensate], like G3BP1, then the interactions between the RNAs are frustrated and clusters stop forming,” – Priya Banerjee.
The researchers describe G3BP1 as a kind of molecular chaperone that scans RNA interactions and prevents them from clustering or clumping inappropriately. This alternative approach erodes the conditions most essential for the formation of clusters. It’s like how a chemical inhibitor prevents crystals from forming in a solution.
“It’s like introducing a chemical inhibitor into a crystal-growing solution; the ordered structure can no longer form properly. You can think of the G3BP1 as an observant molecular chaperone that binds to the sticky RNA molecules and makes sure that RNAs don’t stick to each other,” – Priya Banerjee.
Dissolving Harmful Clusters with Antisense Oligonucleotides
In addition to stopping clusters from forming, the team created targeted engineered antisense oligonucleotides (ASOs). These ASOs are sequentially designed to specifically target and obliterate existing RNA clusters. Upon entering cells, these highly specific ASOs efficiently clear aggregates of RNA, returning them to a soluble, functional state.
“It’s fascinating to watch these clusters form over time inside dense, droplet-like mixtures of protein and RNA under the microscope. Just as striking, the clusters dissolve when antisense oligonucleotides pull the RNA aggregates apart,” – Priya Banerjee.
The potential to personalize and design ASOs that selectively bind to repeat RNAs is exciting for therapeutic developments. This specificity may make them safer, more viable potential treatments for neurodegenerative diseases marked by toxic RNA clumping.
“This suggests our ASO can be tailored to only target specific repeat RNAs, which is a good sign for its viability as a potential therapeutic application,” – Priya Banerjee.
