Scientists design new RNA therapy to bypass mutations behind thousands of genetic diseases

A small error in genetic instructions can bring protein production to an abrupt halt. Instead of building the complete molecule a cell needs, its machinery encounters a premature stop signal and produces a shortened protein, or sometimes almost none at all.

Scientists at the University of Toronto have now developed an RNA-based approach designed to get past those faulty stop signs. By chemically modifying transfer RNA, or tRNA, and packaging it inside specially designed lipid nanoparticles, the researchers restored full-length proteins in laboratory, animal and patient-derived models of cystic fibrosis.

The study focuses on so-called nonsense mutations, which account for about 11% of inherited genetic disorders. Because the same types of premature stop signals can occur across many different genes, the approach could eventually offer something unusual in genetic medicine: one therapeutic strategy potentially applicable to multiple diseases.

“There are so many types of disease-causing mutations – many affecting only a small number of people – that developing a separate gene therapy for every individual mutation is extremely challenging,” said study lead Bowen Li, an associate professor in the University of Toronto’s Leslie Dan Faculty of Pharmacy.

“With tRNA therapeutics, our goal is to develop a common therapeutic approach that could potentially address the same type of mutation across many different genes and diseases, including rare conditions that currently have few or no effective treatment options.”

Cells normally read messenger RNA three genetic letters at a time. Transfer RNAs recognize those instructions and bring the appropriate amino acids to the ribosome, which links them together to make proteins.

A nonsense mutation changes that process by introducing a premature termination codon. The cellular machinery stops reading before reaching the true end of the instructions, leaving the protein incomplete.

The Toronto team engineered suppressor tRNAs, or sup-tRNAs, whose anticodons recognize these premature signals and allow translation to continue. Unlike genome editing, the approach works at the RNA level and does not permanently alter DNA.

“The same type of premature stop signal can occur in many different genes, causing diseases that affect the lungs, brain, muscles and other tissues,” Li said. “Our long-term goal is to develop tRNA medicines that recognize these shared stop signals, so that one therapeutic strategy could potentially be applied across many different genetic diseases.”

Making a suppressor tRNA was only part of the challenge. Earlier versions have faced problems including limited activity, short functional lifetimes, immune activation and difficulty reaching the right tissues.

Natural tRNAs carry numerous chemical modifications that influence their shape, stability and interactions with the cell’s protein-making machinery. Study co-lead Haissi Cui, an assistant professor of chemistry at the University of Toronto, helped investigate whether putting some of those features back into engineered tRNAs could improve their performance.

The team systematically tested modifications at different locations. One, called N1-methyladenosine, or m1A, produced particularly strong results when placed at position 57 or 58.

In an arginine suppressor tRNA, the modification increased premature-stop readthrough by about 10.6-fold. It also improved attachment of the correct amino acid, prolonged the RNA’s functional persistence and reduced innate immune activation.

“We used nature as our design guide and found that adding one specific modification made the engineered tRNA more active and longer-lasting,” Cui said. “It shows what becomes possible when chemistry and RNA biology come together.”

In cell experiments, one modified suppressor tRNA had an estimated apparent half-life of about 29 days, compared with roughly 12 days for its unmodified counterpart. Reporter activity from the modified RNA remained detectable after 30 days, and experiments in mice also showed activity lasting beyond 30 days.

Those gains would mean little without a way to get the molecules into relevant cells. The researchers turned to lipid nanoparticles, the fatty particles also used to carry mRNA in COVID-19 vaccines. But particles designed for other RNA cargo did not necessarily work well for tRNA.

“No matter how powerful you make those tRNAs, without delivery, they cannot be a drug,” said Jingan (Charles) Chen, a PhD candidate and co-lead author.

The researchers screened more than 1,000 ionizable lipids and found that performance differed substantially depending on whether the cargo was tRNA or mRNA. Their search produced TTP-3, short for tRNA-tailored pulmonary delivery–3.

After delivery into mouse lungs, about 60% of cells containing the tracked tRNA were epithelial cells. TTP-3 also reached several airway populations relevant to cystic fibrosis, including 22% of ciliated cells, 19% of club cells and 32% of basal cells. About 15% of rare ionocytes were reached as well.

“That cargo-specific delivery system is one of the major advances of our study,” Chen said. “We used a tailored lipid nanoparticle delivery system that is specifically developed for tRNA.”

Cystic fibrosis gave the researchers a practical test because about one in 10 patients has a nonsense mutation. Drugs such as Trikafta can improve the function of CFTR protein, but nonsense mutations may prevent enough full-length protein from being produced for those drugs to act on.

In human bronchial epithelial cells carrying CFTR nonsense mutations, modified suppressor tRNAs restored CFTR protein and its chloride-channel activity. In cells carrying the R1162X mutation, substantial CFTR levels remained for more than 40 days.

The team also studied intestinal organoids grown from tissue donated by one cystic fibrosis patient with a complex genotype containing four CFTR variants, including two nonsense mutations. Neither Trikafta nor the suppressor tRNAs produced substantial functional recovery alone, but combining them significantly improved CFTR activity. The tRNA restored full-length protein production, giving Trikafta a protein it could then act upon.

That patient-derived experiment involved only one participant, making it a proof of principle rather than evidence that the combination will work broadly. Further testing across different genotypes will be needed.

The researchers also found encouraging signs of selectivity. Ribosome profiling detected no global increase in readthrough at normal stop codons. Mouse safety experiments showed transient, dose-dependent lung inflammation at higher doses, while lower doses remained closer to controls. No detectable liver toxicity appeared in the measurements reported.

Clinical development still presents major challenges. Different organs will require specialized delivery systems, repeated dosing must remain safe, and additional chemical modifications and tRNA designs need testing. The current experiments remain preclinical.

For lung delivery, however, the team has already taken an early step toward a potentially more practical treatment. TTP-3 nanoparticles retained some activity after nebulization, although performance fell and further optimization is needed. That raises the possibility that a future version could be inhaled rather than injected.

“This is the kind of foundational research that medical breakthroughs are built on,” said Lisa Dolovich, dean of the Leslie Dan Faculty of Pharmacy. “By tackling the science and the delivery together, we’re closer to turning a discovery into a drug.”

These studies explore other efforts to overcome premature stop mutations, including engineered suppressor tRNAs, genome editing and treatments aimed at restoring functional proteins in cystic fibrosis and other inherited diseases.

An engineered UGA suppressor tRNA gene for disease-agnostic AAV delivery: Researchers developed an engineered suppressor tRNA targeting the UGA premature stop codon and delivered its gene with an adeno-associated virus, demonstrating another disease-agnostic route toward treating disorders that share the same nonsense mutation type. (Nature Biotechnology, 2026)

Engineered tRNA reduces vision loss in a mouse model of Leber congenital amaurosis: This study used an engineered suppressor tRNA to restore a full-length ion-channel protein in patient-derived retinal cells and partially recover retinal function in mice, extending the therapeutic concept beyond lung disease. (Signal Transduction and Targeted Therapy, 2026)

Prime editing-installed suppressor tRNAs for disease-agnostic genome editing: Researchers used prime editing to convert endogenous tRNAs into suppressor tRNAs, restoring proteins in models of cystic fibrosis, Batten disease and Tay-Sachs disease while also rescuing disease pathology in a mouse model of Hurler syndrome. (Nature, 2025)

AAV-delivered engineered suppressor tRNA rescues visual function in mice with an inherited retinal disease: Engineered suppressor tRNA delivered with an adeno-associated virus restored RPE65 protein expression and improved visual function in a mouse model, with effects lasting at least 36 weeks and little detected readthrough at normal stop codons. (Nature Communications, 2025)

Translation velocity determines the efficacy of engineered suppressor tRNAs on pathogenic nonsense mutations: This research examined why suppressor tRNAs work better against some premature stop mutations than others, showing that local sequence context and translation speed can strongly influence readthrough efficiency. (Nature Communications, 2024)

Research findings are available online in the journal Science.

The original story "Scientists design new RNA therapy to bypass mutations behind thousands of genetic diseases" is published in The Brighter Side of News.

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