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We have all heard of messenger RNA (mRNA) by now, but what about transfer RNA (tRNA)? Well, there is a growing awareness that this emerging technology is capable of a myriad of biological functions linked to human health, and it turns out that it could just be the answer to treating genetic conditions like cystic fibrosis, muscular dystrophy, and genetic epilepsies, among others.
Although tRNA therapies have not yet reached the clinic, preclinical research suggests that this new class of drugs has enormous potential, with one singular tRNA therapy potentially able to treat thousands of different genetic diseases caused by specific mutations.
In this article, we explore tRNA in closer detail, looking at its function, how it can treat genetic diseases, and which companies are currently working on advancing tRNA therapies.
Table of contents
What is tRNA?
mRNA plays a crucial role in transmitting genetic information from DNA to the ribosome, the large molecular machinery responsible for cells’ protein-making. But it cannot do this without the help of tRNA, which is a special kind of RNA molecule that essentially acts like a molecular “bridge” between mRNA and the growing chain of amino acids that make up a protein, helping cells to assemble proteins from amino acids by translating the nucleotide code of mRNA.
To do this, each tRNA molecule reads a sequence of three consecutive nucleotides, called a codon, which encodes for a specific amino acid, representing instructions for adding the amino acid to a protein. As its name suggests, the tRNA then transfers the corresponding amino acid to the ribosome. This process repeats along the length of the mRNA strand until the ribosome runs into a stop codon, a special sequence of three nucleotides that signals the end of the protein-making instruction manual.
The promise of tRNA therapeutics for genetic diseases
But how exactly does tRNA play a role in treating diseases?
Since their initial description in 1958, tRNAs have largely been viewed as intermediaries in the translation of the genetic code into proteins. But recent research has revealed that, although protein translation is their predominant role, tRNAs perform many more functions within the cell that dictate both health and disease.
This is particularly true when it comes to their role in genetic diseases. In certain conditions, genetic mutations can cause “typos” that change one codon to another, prompting a tRNA to add the wrong amino acid, and ultimately leading to proteins that are fully formed but do not function properly.
More significantly, some mutations create premature stop codons. The four nucleotides in mRNA form 64 unique codons, comprising 61 sense codons and 3 stop codons. Certain gene mutations can convert 18 of the 61 sense codons into stop codons. When this happens, the tRNA does not bind these codons, meaning the ribosome mistakenly thinks it has finished its job, resulting in the premature termination of protein translation and the development of dysfunctional disease phenotypes. These mutations – known as nonsense mutations – account for approximately 11% of genetic diseases, making them a major disease-causing mutation in the overall human population.
tRNA therapy could potentially help to counteract the effects of these mutations. The focus of current research is designing “suppressor” tRNAs that can bypass these premature stop signals and incorporate desired amino acids instead. In theory, just one tRNA therapy of this kind could treat thousands of different rare genetic disorders that are caused by the same types of nonsense mutations that result in faulty gene expression.
The idea of suppressor tRNA first came about in 1965, after researchers experimentally demonstrated that it could recognize stop codons and insert amino acids, thereby bypassing the translation termination process. Subsequent studies further revealed the readthrough mechanism of suppressor tRNA in eukaryotes and showed its potential in gene therapy. The first in vivo experimental study of suppressor tRNA was reported in 2000, successfully inducing readthrough in mice through local injection.
More recently, with the advancement of genetic engineering technologies, the efficiency of synthesizing and modifying suppressor tRNA has improved. Representative studies reported in 2022 and 2023 demonstrated the systemic delivery of suppressor tRNA using adeno-associated virus (AAV) and lipid nanoparticles (LNP) to treat diseases related to nonsense mutations.
Yichen Hou, a graduate student studying tRNA biology at the University of Chicago (UChicago), told UChicago’s news department last year – after a promising tRNA study conducted by researchers at the university – that this type of therapy is an attractive option compared to other types of gene therapy because the molecules are very small, compact, and stable, making them relatively easy to deliver to cells. She said it is also possible that tRNA could be effective at lower doses for certain diseases, which will help to minimize side effects. Plus, even if side effects do occur, tRNA therapy is not permanent like DNA editing technologies are, so treatment could be paused for reevaluation or modification if necessary.
tRNA therapeutics companies: Alltrna and Tevard Biosciences lead the way in the field
The recent progress being made in tRNA research has started to attract some attention within the biotech industry, with some startups making it their mission to be the first to develop successful tRNA therapies to take into the clinic.
Alltrna presents positive preclinical data for its first tRNA candidate for stop codon disease
Rather than focusing on one particular genetic disease, Flagship Pioneering company Alltrna is focused on treating stop codon disease – in other words, it wants to engineer a tRNA therapy that can correct the premature stop codon mutation associated with a number of different diseases.
The company emerged from stealth in 2021 equipped with the technologies needed to express, synthesize, modify, and quantify tRNA molecules, as well as machine learning tools to thoroughly explore the sequence and modification space to optimize their biology. Michelle C. Werner, chief executive officer (CEO) of Alltrna, told Technology Networks that this platform has proven critical to the company’s efforts to tune the therapeutic properties of tRNAs, whether that be related to efficacy and safety, or more pharmacological characteristics like stability, solubility, and deliverability.
Alltrna’s tRNA technology has already received positive results in preclinical studies. In December 2024, the company presented preclinical data demonstrating proof-of-concept, showing that the company’s first engineered tRNA oligonucleotide candidate, AP003, restored protein production to clinically meaningful levels in two disease models driven by the same premature termination codon.
According to Werner in Technology Networks, the company is also exploring and optimizing the design of tRNA delivery vehicles that help ensure these molecules are able to reach their tissue targets without being destroyed by nucleases and other defense mechanisms within the body. To start with, the company is focusing on lipid nanoparticles, due to the extensive experience with the mRNA vaccines against COVID-19. Indeed, AP003 is encapsulated in a clinically validated, liver-directed lipid nanoparticle.
This delivery method has also partly resulted in Alltrna’s initial focus being on the genetic liver diseases, which include upward of 400 different rare and ultra-rare diseases, as RNA treatments already have a proven ability to reach liver tissue when encapsulated in lipid nanoparticles. Looking further into the future, the company will look to prioritize diseases based on its ability to target tissues outside of the liver.
Werner also noted in the interview with Technology Networks that, although Alltrna’s initial focus is on stop codon disease, the company believes that there are opportunities to extend these efforts to other types of genetic changes that disrupt protein production, such as frameshift mutations – caused by a deletion or insertion in a DNA sequence that shifts the way the sequence is read – or missense mutations – alterations in the DNA that results in a different amino acid being incorporated into the structure of a protein.
In 2023, the company raised an impressive $109 million in series B funding, suggesting that there is some investor interest around tRNA therapies, which is likely to increase if this class of therapeutics actually shows success in the clinic.
Tevard Biosciences collaborates with Vertex to develop tRNA therapies for DMD
Founded by MIT molecular cell biologist Harvey Lodish, along with Daniel Fischer and Warren Lammert, who are parents of children with Dravet syndrome, Tevard Biosciences’ goal is to develop tRNA therapies that can ultimately cure Dravet and other genetic disorders in which tRNA plays a role in disease progression.
Tevard is actually working on two different types of tRNA-based therapies. One of these is suppressor tRNA therapy intended for diseases caused by nonsense mutations. By using a viral vector to express a patented tRNA in targeted cells, the company can insert the normal amino acid at the site of the premature stop codon, thereby generating a functional protein. As with Alltrna, just one of Tevard’s suppressor tRNA therapies is expected to be able to treat multiple diseases.
The second type of tRNA therapy that Tevard is working on is called “enhancer” tRNA. This is meant for diseases caused by haploinsufficiency, which occurs when one copy of a gene is inactivated or deleted and the remaining functional copy is not adequate to produce the necessary gene product to preserve normal function. To correct this, Tevard uses a viral vector to overexpress a unique combination of endogenous tRNAs in targeted cells, in turn increasing the amount of protein produced by the functional gene copy to normal levels by increasing the stability, and therefore half-life, of its mRNA.
Both of these therapies have the potential to cure Dravet. In 85% of cases, this severe form of epilepsy is caused by haploinsufficiency of the SCN1A gene. Meanwhile, more than 20% of mutations that cause Dravet are due to premature stop codons, causing production of a nonfunctional protein fragment. Due to its large size, the SCNIA gene cannot be delivered by common viral vectors, and over-expressing SCN1A can have damaging effects, making tRNA therapies a potentially better way to treat Dravet than traditional gene therapy approaches.
In March 2023, Tevard announced a four-year global research collaboration with Vertex Pharmaceuticals to develop novel tRNA-based therapies for Duchenne muscular dystrophy (DMD) caused by nonsense mutations, with options to expand into additional muscular dystrophies and a second indication. As part of the deal, Tevard is advancing the research and discovery of novel tRNA-based therapies, with all program costs funded by Vertex, and Vertex is responsible for all subsequent development, manufacturing, and commercialization.
Tevard is currently focused on its preclinical pipeline. In August last year, it also said that it would be moving its headquarters to Lilly Gateway Labs (LGL), which is housed within one of Eli Lilly’s newest research and development (R&D) facilities in Boston Seaport, the Lilly Seaport Innovation Center. Tevard was selected to join the LGL community based on its “cutting-edge tRNA platform technologies and promising programs for neurological disorders, cardiology, and muscular dystrophy.”
The future of tRNA therapies: Overcoming challenges and progression into clinical trials
Although Alltrna and Tevard appear to be progressing with their tRNA therapies, it has not all been plain sailing for everyone working in the field. The recent closure of HC Bioscience is a prime example of this. The company had been working on a lead preclinical tRNA program for the treatment of severe hemophilia A, with other early-stage candidates taking aim at DMD and cancer. But after conducting animal studies for its lead asset, the company decided to discontinue the development of the program, ultimately having to shut its doors for good.
“After completing key animal studies for our hemophilia A program utilizing tRNA-based technology, we conducted a thorough assessment of the data,” said HC’s CEO and co-founder, Leslie Williams, in a statement to Fierce Biotech last month. “Given the challenges in targeted delivery and other factors, we made the difficult decision to discontinue development of the program.”
Indeed, precisely delivering tRNA to its target is an obstacle in the field, partly due to its negative charge and susceptibility to degradation. Developers need to prove that their tRNAs will not accidentally be delivered to the wrong target and will not interfere with normal genes, which can potentially trigger adverse events.
Having said that, significant progress has been made in both viral and non-viral delivery systems, offering feasible options for delivering various RNA payloads and targeting different tissues. The advent of COVID-19 vaccines showed how lipid nanoparticle technology is particularly suitable for the delivery of RNA therapies, which, as mentioned previously, is what Alltrna is using to deliver its tRNA therapies.
If these challenges can be overcome by the likes of Alltrna and Tevard, we could soon see tRNA therapies enter the clinic. One of the hurdles here is designing basket trials that can group patients with different diseases but with the same underlying genetic mutation – a trial design that is commonly used in oncology but has been less explored in rare diseases.
Werner told Pharmaceutical Technology that Alltrna is working closely with global regulators, including the U.S. Food and Drug Administration (FDA) and European Medicines Agency (EMA), to navigate the complexities of designing such trials. She also noted that regulators recognize the challenges of drug development for ultra-rare patients and are encouraging strategies that can address multiple diseases at once.
Only time will tell whether tRNA will be successful in clinical trials, but, for now, it is fair to say that this class of drugs is certainly starting to show promise for its ability to tackle devastating genetic diseases that might be unsuitable for traditional gene therapy.
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