New ‘pothole-filling’ RNA strategy targets the genetic root of DM1
Scientists design hybrid molecule that untangles toxic RNA, frees vital proteins
Using a “pothole-filling” strategy that combines the precision of DNA-like strands with the versatility of small molecules, scientists have designed a new type of therapy that can target the mutant genetic material that causes myotonic dystrophy type 1 (DM1).
This hybrid approach allows scientists to stabilize tangled RNA structures and prevent them from trapping vital proteins, potentially offering a more effective way to treat the disease’s root cause.
“This discovery paves the way for developing highly selective, structure-based RNA therapies with fewer side effects and broader applications,” Danith Ly, PhD, senior author of the study at Carnegie Mellon University, said in a university news story. “With its precision-targeting capabilities, this approach represents a promising step toward developing effective, disease-modifying therapies for patients suffering from these debilitating genetic disorders.”
The scientists described their new approach in PNAS, in a paper titled “A pothole-filling strategy for selective targeting of rCUG-repeats associated with myotonic dystrophy type 1.”
The genetic roots of DM1
DM1 is the most common form of muscular dystrophy with symptom onset in adulthood. This genetic disease is caused by mutations in the DMPK gene. Specifically, DM1 occurs when three nucleotides (the building blocks of DNA) in the DMPK gene are repeated an excessive number of times.
When a gene is read, the abnormal repeat is copied over into a molecule called messenger RNA (mRNA). Normally, mRNA serves as a temporary intermediary during protein production. But in DM1, the abnormal repetitive sequence forms tangled structures, and proteins normally important for RNA processing become trapped in the tangles. This leads to widespread RNA processing problems in the cell, ultimately driving disease progression.
In this study, the researchers were working on a so-called “pothole-filling” approach for DM1 treatment. The basic idea is to design a molecule that can bind to these disease-causing RNA stretches and prevent them from interfering with the cell’s RNA processing machinery — similar to how a pothole on a road can be filled to prevent a vehicle’s tire from falling in.
In theory, there are two main biochemical tools that could be used to target the disease-causing RNA in DM1. One approach is to use small molecules, or tiny compounds that are specifically designed to fit into the cracks and crevices of a target molecule. However, designing small-molecule therapies to target RNA is extremely difficult because RNA strands don’t have consistent molecular nooks and crannies that small molecules can specifically fit into.
An alternative approach is to use antisense oligonucleotides, which are basically short strands of nucleotides. Since they’re also made of nucleotides, these therapies can bind to RNA molecules via hydrogen bonding, the same type of chemical interaction that allows two strands of DNA to form the famous double helix. However, on a molecular scale, antisense oligonucleotides are big and bulky.
The scientists’ new approach basically aimed to combine the best features of both small molecules and antisense oligonucleotides to “simultaneously enhance RNA-targeting precision, maintain specificity and selectivity, and provide synthetic versatility, advancing the development of effective RNA-based therapeutics,” they wrote.
The researchers designed a short sequence of three artificial nucleotides, small enough to resemble a small molecule but also able to form hydrogen bonds with the mutant RNA that drives DM1. And notably, whereas traditional antisense oligonucleotides bind to single RNA strands, these molecules were designed so they’d simultaneously bind to two strands, making them better at wiggling into the RNA tangles that cause DM1.
“These ligands insert themselves between the two RNA strands, in contrast to the conventional antisense approach, which requires unwinding the RNA secondary and tertiary structures,” Ly said.
Success in patient cell models
The scientists conducted a battery of molecular tests to demonstrate that their new molecules could interact as intended with mutant DMPK RNA while not interfering with the cells’ healthy RNA.
“The ability to selectively target [disease-causing] RNA repeats without affecting normal [RNA] highlights the downstream therapeutic and diagnostic potentials of this approach,” the researchers wrote.
In experiments using cells derived from DM1 patients, treatment with the new molecules led to improvements in RNA processing. The scientists noted that much more work is needed to validate and refine this approach, but they are hopeful that their new molecules could be developed into treatments for DM1 and other diseases caused by mutations with abnormally repeated genetic sequences.
“Diseases like myotonic dystrophy, Huntington’s disease and fragile X syndrome, which have complicated, life-stealing symptoms, are caused by the repeat of only three nucleobases, which seems so simple,” Ly said. “If we can stop proteins from being sequestered in this hairpin, we believe we can help improve the symptoms of these diseases.”
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