New RNA Therapy Promises Treatment for Neuromuscular Disorders

Researchers from Carnegie Mellon University have discovered a way to target RNA that could lead to new treatment options for myotonic dystrophy type 1 (DM1), the most common adult-onset form of muscular dystrophy, and other RNA-repeat expansion disorders. "This discovery paves the way for developing highly selective, structure-based RNA therapies with fewer side effects and broader applications," said Danith Ly, a professor of chemistry in the Mellon College of Science and director of the Institute for Biomolecular Design and Discovery. "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 research is published in the journal Proceedings of the National Academy of Sciences. What causes muscular dystrophy? Conditions like DM1 happen when certain RNA sequences repeat too many times, forming harmful structures that interfere with normal cell function. The researchers' new approach provides a powerful and versatile solution for precise RNA targeting, paving the way for the development of RNA therapies with fewer side effects for disorders such as spinocerebellar ataxias, Friedreich's ataxia and amyotrophic lateral sclerosis (ALS). DM1, which affects at least 1 in 2,300 people worldwide, mainly causes progressive muscle loss, weakness and myotonia but it can also affect other parts of the body, including the heart, lungs and eyes. There is currently no effective treatment. DM1 is caused by a mutation in the DMPK gene, which leads to an abnormal increase in a repeated section of genetic code, known as CTG repeats. This genetic "stutter" occurs when the body's instructions become stuck on repeat. In people without DM1, this CTG sequence is repeated between five to 35 times. In a person with DM1, the number of repeats can be in the thousands. When the gene is transcribed into RNA, the chain of repeats forms a hairpin loop—a tangled structure that functions like a sticky trap for essential proteins. These proteins, which play a vital role in RNA splicing, become sequestered or trapped within the loop. The trapped proteins cannot do their jobs, creating a cellular traffic jam that interferes with the production of many other proteins in cells. Ultimately, this disruption causes the symptoms of DM1, with a higher number of repeats typically resulting in more severe symptoms and an earlier onset. "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." A molecular 'pothole filler' for toxic RNA Ly likens his team's latest discovery to a "pothole filler"—a solution that fits neatly into damaged spots without disturbing the rest of the road. In this case, the damage is caused by toxic CTG RNA repeats. In the new research, Ly and his team, including Shivaji Thadke, a former postdoctoral associate, Dinithi Perera, a Ph.D. graduate, and Savani Thrikawala, a third-year Ph.D. student, created small, highly specific molecules called nucleic acid ligands that precisely recognize and bind to these disease-causing RNA stretches without disrupting healthy RNA. The approach is more precise and less likely to produce side effects than conventional small-molecule drugs and antisense therapies currently under development. Such traditional therapeutic approaches often struggle with specificity, according to Ly, either failing to distinguish between normal and pathogenic RNA or requiring complex modifications for effective delivery. The new nucleic acid ligands overcome these challenges through a bifacial recognition mechanism, which ensures precise targeting of pathogenic repeats while minimizing off-target interactions. A double-sided molecular strategy Central to the design of Ly's novel RNA-targeting approach are gamma peptide nucleic acids and bifacial (Janus) bases. Ly and his colleagues in Carnegie Mellon's Center for Nucleic Acids Science and Technology are leaders in creating and developing peptide nucleic acids (PNAs), synthetic molecules that contain the same nucleobases as RNA and DNA. PNAs can be programmed to correspond to genetic sequences that cause disease, allowing them to hunt down and bind with detrimental sequences. In 2014, CNAST began to develop the next generation of PNA technology. Ly turned his focus to developing PNAs with Janus bases. Named after the two-faced Roman god Janus, PNAs are double-sided, allowing them to bind to both strands of a DNA or RNA molecule. "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. In laboratory models, the lead ligand, LG2b, demonstrated remarkable selectivity for disease-causing RNA sequences, displacing harmful protein-RNA complexes without interfering with normal gene function. The research team is continuing to work with their ligands, optimizing them to enhance cellular uptake, refining drug delivery methods and evaluating their efficacy in preclinical disease models. Ly published along with Thrikawala,Thadke, Perera and CMU alumna Isha Dhami, as well as researchers at the Indian Institute of Science, Georgia State University and Nanyang Technological University, Singapore.