Opinion: Leveraging tRNA to Scale Genetic Medicines for Rare Diseases and Beyond

Transfer RNA_Alltrna

Pictured: tRNA matches the codon in mRNA to the correct amino acid as specified by the rules of the genetic code and transfers the amino acid onto the growing polypeptide chain to make a protein. Engineered tRNAs could be used to treat any disease caused by a premature termination codon, which is treated as a stop signal by the translational machinery/Alltrna

The success and rapid evolution of the messenger RNA COVID-19 vaccines and the impact of FDA-approved small interfering RNA medicines like Onpattro are clear indications that the era of RNA-based medicines is well upon us. The sequence specificity of these products goes a long way to providing highly effective therapy against a variety of diseases while also reducing the safety risks associated with small molecule drugs.

And yet, that same sequence specificity limits treatments to a single or small number of genetic disorders. In major, common diseases, the costs associated with drug development and delivery can be spread over many patients. But for the vast majority of genetic disorders—such as the rare and ultra-rare diseases that impact hundreds or thousands of patients globally—the costs have been prohibitive, leaving these patients untreated or with therapies that manage symptoms rather than their disease.

There is another RNA molecule, however, that can help address this problem, one that has not yet been extensively explored for its therapeutic potential except by a small handful of companies and research groups: transfer RNA (tRNA).

The unique biology of tRNA means that it may be possible to completely redefine treatable patient populations, based not on disease pathology or the mutated gene but rather on the mutations themselves, mutations shared not by hundreds or thousands of patients but by millions. This mutation-specific, gene-agnostic approach promises to make the once clinically and economically unfeasible feasible.

The Unique Roles of tRNA in mRNA Translation

tRNA is best known for its central role in translating genetic code carried by messenger RNA (mRNA) into the proteins that provide the molecular machinery of the cell. The genetic code takes the form of base triplets known as codons, each of which represents an amino acid in the final protein or a signal to stop translation. Each codon is recognized by tRNAs carrying the appropriate amino acid that is then added to the growing protein chain.

Mutations in these codons can introduce an incorrect amino acid (missense), delete or insert nucleotides that alter the reading frame (frameshift), or create a premature termination codon (PTC) that signals the end of protein translation too early. Such mutations generate aberrant proteins that lose biological function and may be toxic, triggering diseases ranging from sickle cell and cystic fibrosis to Duchenne muscular dystrophy and Rett syndrome.

Universal Therapeutic Potential

It is estimated that 30 million people have one of the hundreds of diseases caused by any of the three PTC mutations—what we’ve defined as Stop Codon Disease—making the search for treatments that would overcome premature translation termination a key focus of drug development. A handful of small molecule drugs have been developed to facilitate PTC readthrough and protein synthesis, but their success has been limited.

Nature, however, has provided a mechanism to promote PTC readthrough using suppressor tRNA molecules modified to recognize the PTC as though it were an amino acid-encoding sequence. These natural suppressor tRNAs served as the starting point for concerted efforts to engineer and test generations of tRNAs designed to facilitate PTC readthrough in a therapeutic context.

By focusing attention on the PTC triplet rather than the mutated gene (in contrast to, for example, gene replacement or gene editing), an individual tRNA-based drug can be used for all diseases triggered by that PTC mutation. In May, for example, Alltrna announced it had engineered a tRNA molecule targeting a specific PTC mutation that demonstrated universal readthrough in 25 disease models across 14 different genes and seven different mutation locations within a single gene.

In principle, a very similar approach could be used to address the impacts of missense and frameshift mutations or rare codons, modifying the tRNA to recognize those codons and/or re-establish the reading frame or adjusting the levels of a given tRNA to increase the likelihood of incorporating the preferred amino acid into the polypeptide chain.

Realizing the Potential of tRNA Medicines

Much of tRNA biology is still being deciphered. For example, the structures of tRNA molecules influence characteristics such as molecular stability and interactions with enzymes involved in making tRNAs functional. And just like DNA, tRNA is heavily modified with chemical groups that can alter traits such as protein translation efficiency and resistance to nucleases.

Understanding more deeply how these features influence tRNA function and its physicochemical and pharmacological properties will demand the continued evolution of technologies and methods to engineer, synthesize and test vast libraries of molecules in a variety of contexts. And given the sheer diversity of molecules possible, machine learning tools will be invaluable in deciphering patterns within the data to guide each subsequent generation of leads. Such advances are central to Alltrna’s platform.

The task is large, and so is the potential to help develop new medicines for the more than 300 million people with one of the 6,000 genetically defined diseases. A mutation-specific, gene-agnostic approach will not only dramatically scale the creation of new genetic medicines but also place the treatment of rare and ultra-rare diseases within reach, offering hope for the 95% of patients for whom there are currently no disease-modifying treatments.

Michelle C. Werner is CEO of Alltrna and CEO-partner at Flagship Pioneering. She is an experienced pharmaceutical executive with more than 20 years in the industry spanning commercial and R&D. Michelle is a wife and mother to three children and is a member of the rare disease community.

Update, Dec. 11: This story was first posted with the headline: "Opinion: Move Over mRNA; tRNAs Have Even Broader Reach." 

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