Jonathan D. Grinstein, PhD, the North American Editor of Inside Precision Medicine, hosts a new series called Behind the Breakthroughs that features the people shaping the future of medicine. With each episode, Jonathan gives listeners access to their motivational tales and visions for this emerging, game-changing field.
In May of 2020, drug developer Michelle Werner learned that one of her three children, her middle child Caffrey, was diagnosed with Duchenne muscular dystrophy (DMD). Werner went searching for an existing or experimental cure but came out empty-handed. So, after a couple of decades as a big pharma stalwart, Werner made a major career change and took over as CEO of Flagship Pioneering company Alltrna, which had a solution she believed could help not only Caffrey but also other children and families in the same position.
In this Behind the Breakthroughs episode, Werner talks about the experience of being a mother to a child with a rare disease and her mission as Alltrna CEO: to find cures for all rare diseases, the majority of which have no approved therapies. Michelle explains how Alltrna’s engineered transfer RNAs (tRNAs) function and how they can be used for many diseases caused by mistakes in the genetic code that create early stop signals.
Highlights of this interview have been edited for length and clarity.
IPM: How do Alltrna’s engineered tRNAs work?
Werner: The concept behind Alltrna, which sucked me in from day one, is that a single one of our engineered tRNAs may be able to address hundreds, if not thousands, of different genetic conditions because we focus on the common mutations that we observe across all of these different diseases. We don’t focus on the individual disease, gene, or protein that’s affected. It has this way of becoming a universal tool to address a very fragmented problem, but simplifying that fragmented problem into a few universal diseases that can be addressed with a tRNA. And that felt like a profoundly effective way to tackle the awful challenge of 10,000 different diseases, all of which require innovations that will make a significant difference for patients.
The role of a tRNA is the same regardless of whether it’s the dystrophin gene or if it’s the gene that codes for PKA, which is the protein relevant in phenylketonuria, or Factor IX in hemophilia. Because it performs this function across the entire coding sequence, it has the same effect when it comes to mutations: it can address mutations regardless of the location where the mutation occurs in the coding sequence. We are starting with our tRNA by focusing specifically on nonsense mutations, which are when a codon that codes for one of these amino acids instead codes for a stop. That happens somewhere along the coding sequence where it should not be. Because there are no natural tRNAs that can read these premature termination codons, what ends up happening is that the protein translation process terminates too early, the tRNAs don’t exist to understand what to do at that mutation, and the result is that you’ve got this truncated protein, often a dysfunctional protein or an absent protein, and that’s what causes disease in those circumstances.
What we’re doing is engineering tRNAs that do not exist in nature but are inspired by nature that actually know how to bind these premature termination codons. So instead of stopping translation, the tRNA says, “I know that an arginine is supposed to be here instead of a stop, so I’m going to insert the arginine into the growing protein chain,” and then the protein translation process continues as it normally would have had that mutation not been in there in the first place.
IPM: How do Alltrna’s engineered tRNAs compare with genetic medicines, such as gene replacement therapy and gene editing?
Werner: Gene replacement therapy in Duchenne does exist now, which is fantastic, and the community is very grateful for that innovation. However, due to the size of the protein, it’s a mini version of the gene and, consequently, a mini version of the protein. While this may be beneficial for patients, it will also have limitations. However, those gene replacement therapies are only applicable to DMD; they can’t be used for other diseases because they’re highly gene-specific. Gene editing is similar in that it is specific to a certain gene and location for where mutations occur, as it relies on the guide sequences of the flanking regions to identify where those edits need to be made. For mRNA, it’s the same thing.
Now, tRNA doesn’t have that limitation. What we’ve been able to demonstrate with our platform is that, with the same engineered tRNA, we’ve been able to read through over 25 different reporter gene models in vitro, which cover more than 10 or 12 different diseases. We also examine approximately seven different locations where mutations occur, using the same engineered tRNA. The engineered tRNA can address and read through those mutations, restoring a full-length, functional protein, regardless of the gene, disease, protein, mutation, location, or tRNA function, because it operates universally.
Duchenne is a fascinating example of a field we hope to enter in the future, as I am not aware of another way to restore full-length dystrophin. Given the size of the gene and the size of the protein, it will have limitations. As I have already mentioned, mRNA gene replacement therapy would never be a viable option for Duchenne due to the enormous size of the protein. If gene editing emerges as a viable treatment for Duchenne, it’s likely to employ an exon-skipping strategy. So, it wouldn’t be a full-length, wild-type version of the protein.
IPM: Are there any off-target concerns for Alltrna’s engineered tRNAs?
Werner: In reality, the likelihood of a nonsense mutation causing a disease increases if it occurs in other genes. So, we’re talking about monogenic genetic diseases—when the nonsense occurs in a specific gene, it is the cause of the disease. There aren’t nonsense mutations out there that do not cause these types of conditions. As I mentioned, premature termination codons occur at the end of a coding sequence, where it is clear that stopping translation is necessary. You don’t want to have these elongated proteins that go on forever.
We need to ensure that translation stops at the appropriate time, rather than reading through the premature termination codon. The good news is that biology works in our favor here. At the end of the coding sequence, which is where you would have these normal termination codons in pretty much almost every single gene, you would have a normal termination codon if you’ve got the three prime UTR and the polyA tail, which then sort of kind of folds over the end of the coding sequence. And then at the end of the coding sequence, you not only have one termination code, you have multiple—two, three, sometimes up to 40 different stops that are occurring in a row. Therefore, the design of the tail primarily aims to attract release factors, enabling the ribosome to initiate translation termination. And that very much is true even in the presence of an engineered tRNA.
IPM: How are Alltrna’s engineered tRNAs delivered?
Werner: Delivery is a crucial aspect of this process. Our tRNAs are oligonucleotides, and like other nucleic acid-based therapies, they are highly dependent on how you can deliver those payloads to the specific sites that are critical for these diseases.
We are starting with the formulation of lipid nanoparticles containing our tRNAs, which will target rare genetic liver diseases. We believe that tRNA has the potential to address approximately 400 of these diseases. We’ve chosen to formulate an LNP as a strategic choice initially because, thanks to the mRNA COVID vaccines, LNPs have been administered to millions of people worldwide, possibly billions. Several different areas are using them as therapeutics. So, we know exactly how well they reach hepatocytes and how effective and efficient they are. We understand the safety profile, and we have models for other therapeutics that utilize the LNP formulation in a repeat-dose capacity. It was a strategic choice to mitigate delivery risk rather than focus on a novel delivery modality in addition to a novel payload, given that the tRNA has never been present in humans before.
IPM: How are you approaching clinical trials for rare diseases?
My background in oncology is helpful because we see the use of basket trials, which have led to the approval of seven, eight, or nine different oncology therapeutics. We are also seeing this clinical design applied in the rare disease setting. However, in that trial design, patients have fundamentally different diseases; nonetheless, they are all selected because they share the same underlying mutation, which is a genetic driver of their respective diseases. We administer the same therapy to all patients.
In our case, it would be AP003. We measure the same or a similar outcome across those patients as part of the clinical trial. This strategy is particularly important for rare genetic diseases because, as I mentioned, there are 10,000 different diseases, most of which are ultra-rare. One reason we have so few approved therapies—only about 5 to 10% of these diseases—is that the individual patient populations for these ultra-rare diseases are often too small to justify the development of bespoke drugs for a single disease or mutation. That’s why most of these conditions don’t improve much. However, when you use a basket trial strategy, not only can you address the more common genetic diseases, but also, because you’re selecting those common mutations across all these different diseases, you can capture patients in the ultra-rare setting simultaneously.
IPM: How do you juggle all the different roles you play as mother, CEO, and rare disease advocate?
Werner: This has had a profound effect on me. When I first took the job, I thought, “I’m going to have to figure out a way to wear my CEO hat and my rare disease mom hat at different times but be able to create delineation and separation between those two roles, recognizing that that could be a challenge but that it would be important.” I realized fairly early on that maybe it was a mistake to have that feeling. I believe that what I’ve learned in the past three years is that when I wear my mom hat while acting as a CEO, I become a better CEO. And when I wear my CEO hat as a mom, I’m a better mom.
This realization was somewhat unexpected. I’m always a mom. However, when I first took on this role, I quickly realized that it was crucial to identify how we should and could engage with patient groups early on to truly understand the lived experiences of individuals with the conditions we are focused on and to consider this understanding as we develop our molecules and formulate our clinical plans. I had never been involved in oncology at such an early stage before; I may have engaged when we were about to launch, but certainly not during the initial stages of discovery and development. But I probably did that within my first few months. I started to engage with patient advocacy groups.
Being a mom helped me understand the perspectives of patients and caregivers, emphasizing their importance and my desire to integrate these insights into the company’s foundational culture from an early stage. I believe that has led to the development of AP003. This compound is better than we initially thought we could design, so we created this innovative development plan, which we’re now moving to the clinic.
For me, what I would say is that it was just one example of a very unexpected thing that has helped me to appreciate that both of these perspectives are valuable. Not to mention, a profound sense of urgency drives everything we do. Every morning, when I wake up and see my son, I recognize that I’m persistently searching for a transformative solution for him, and I understand that other families dealing with rare genetic liver diseases share a similar desire for their children. And so every single day matters, every single hour and experiment matters. This understanding is deeply embedded in the culture we have here at Alltrna. We all get that, and we’re just making it count because patients don’t have time to wait.
