As a child, before Keith Gagnon knew anything about science, he told his mom he wanted to be a scientist when he grew up. Now, decades later, Dr. Keith Gagnon is a biochemist and molecular biologist specializing in RNA biology, nucleic acid therapeutics, repeat expansion disorders, and CRISPR-Cas systems, serving as an Associate Professor in the Department of Biochemistry at Wake Forest University School of Medicine in Winston-Salem, North Carolina.

From Construction Sites to the Laboratory

As a child, Keith was always intrigued by how things work and would often disassemble electronics. His family moved often, and Keith describes his teenage years as a bit wild and unpredictable. Growing up, he was competitive, and academics were valued in his home. In addition to loving science, he was a standout artist and was involved in athletics, including cross-country running and basketball.

“But what absolutely fascinated me was biology and chemistry,” he says. “I remember reading Campbell’s Biology, 3rd edition, and it just stuck in my head. I was able to memorize it without trying.”

Keith’s parents were a homemaker and a carpenter, and neither had pursued a secondary education. During his high school years, Keith worked in restaurants, and he credits his AP Biology teacher, Ms. Woody, for helping him realize he was good enough to attend college. After graduating, he went on to work in construction, painting, building decks, and plumbing — things he had done every summer with his dad since he was old enough. He also nearly joined the army.

“But I realized these were not what I wanted,” he says. “I wanted to be a thinker. I wanted to solve problems that would have a lasting impact. I wanted to do something big in my life. It brought me back to biology and chemistry, as well as a deeper, somewhat spiritual searching for what really mattered. I think this has driven me. ”

Discovering a Passion for Research

After being accepted to North Carolina State University and deciding a degree in art was not one that would pay the bills, Keith chose to major in Biochemistry. Warmly welcomed into the laboratory of his undergraduate advisor, Dr. E. Stuart Maxwell — a firm and direct man with a wry sense of humor — Keith’s love of laboratory science blossomed.

He continued studying under Dr. Maxwell’s supervision through graduate school and his PhD, focusing on the assembly, structure, and function of archaeal Box C/D small nucleolar ribonucleoproteins (sRNPs) (1).

“He held high expectations for data quality and creative problem solving,” Keith says. “It instilled in me a pure joy for science.”

Finding a Home in Oligonucleotide Therapeutics

Trained in “old school” protein and nucleic acid biochemistry, Keith’s doctoral research focused on RNA biology and RNA-protein interactions, particularly small nucleolar RNAs and their associated protein complexes. After completing his PhD, however, he wanted to apply those fundamental insights to more disease-relevant problems.

That desire led him to the laboratory of Dr. David R. Corey at UT Southwestern Medical Center in Dallas, Texas, where he trained as an NIH Ruth L. Kirschstein Fellow.

“I remember seeing one of his graduate students present at the RNA Society Meeting,” Keith says. “All I knew was they were doing cool RNA-guided biology in the human cell nucleus, and I needed to be there.”

Under Dr. Corey’s mentorship, Keith immersed himself in the rapidly evolving world of nucleic acid therapeutics, exploring nuclear RNA interference (RNAi), antisense oligonucleotides (ASOs), siRNAs, and strategies for targeting repeat-expansion disorders such as Huntington’s disease (2), spinocerebellar ataxia 3, and C9ORF72-associated ALS/FTD.

Keith describes Dr. Corey as patient and generous, giving him room to make mistakes while emphasizing efficiency, timeliness, and always advocating for and encouraging him. The experience shaped the direction of Keith’s career. Among his most recognized contributions is work demonstrating that RNAi mechanisms operate within the cell nucleus (3), as well as his work on the chemical modification of CRISPR RNAs, particularly his obsession with figuring out how to fully chemically modify them.

Building an Independent Research Program

In 2014, Keith launched his own academic research laboratory at Southern Illinois University School of Medicine, holding joint appointments in Biochemistry & Molecular Biology and Chemistry & Biochemistry. In 2023, the Gagnon laboratory officially moved to the Department of Biochemistry in the Wake Forest University School of Medicine.

Although the Gagnon Lab does not exclusively focus on oligonucleotide therapeutics, it employs a multidisciplinary approach that combines biochemistry, biophysics, structural biology, sequencing, cell culture, and nucleic acid chemistry. Over the years, the laboratory has made important contributions to chemically modified CRISPR guide RNAs, anti-CRISPR inhibitors, and high-throughput viral genome sequencing.

Persistence, Creativity, and Doing More with Less

Keith doesn’t hold back when discussing the challenges of scientific research.

“Nine out of ten experiments do not work out the way we anticipate,” he says. “But this is normal. You must be persistent and really creative, especially when you do not have the tools or resources you need.”

Not being flush with resources during graduate school or later when establishing his first independent laboratory forced Keith to become an exceptionally creative scientist.

“You have to be really clever to solve important problems when facing these limitations. And you have to be really careful that it does not limit how big you can think or make you give up easily.”

The Discoveries Shaping the Future of Oligonucleotide Therapeutics

Keith views the successful development of siRNA therapeutics as one of the field’s most important achievements.

“Figuring out how to make siRNAs into potent therapeutics, which involves both chemistry, safety, and delivery, especially GalNAc, was a major milestone,” he says.

He also points to the rapid discovery of biological processes that can be harnessed therapeutically, including splice-switching oligonucleotides, A-to-I editing, and CRISPR-Cas technologies. In particular, he believes prime editing and its newest generations hold enormous potential.

Applications of AI/ML tools, the discovery of new RNA biology that can be leveraged for therapeutics, and the mechanistic level of detail we are converging on for diseases are three things that Keith is excited about. “They will enable us to move more quickly and create better medicines at much lower costs,” he says.

One area Keith believes deserves renewed attention is aptamer technology. Watching a talk on the topic by Bruce Sullenger when he was a first-year graduate student cemented in Keith’s mind the potential of this approach, which uses synthetic antibodies known as aptamers, to bind with high affinity to a specific target.

“Maybe it was ahead of its time,” he says. “For basic science, it works. But broad clinical translation has been out of reach.”

Still, advances in chemistry, target discovery, and selection methods leave him optimistic that aptamers may eventually find their place in medicine.

Keith is equally enthusiastic about the role of artificial intelligence and machine learning in drug development. “We need to accept this reality while also learning to use it very responsibly,” he says.

Rather than replacing scientists, he believes these tools will increase demand for researchers capable of asking good questions, interpreting data, and thinking critically. However, he notes that a potential challenge is the accessibility and democratization of these tools for researchers, and that if they become largely privatized, this would affect the field’s long-term creative and practical progress.

What Still Stands in the Way

While agreeing that delivery remains one of the most cited barriers to broader adoption of oligonucleotide therapeutics, Keith believes another challenge receives less attention: careful experimental design.

“Trying to move too fast or making too many assumptions about underlying mechanisms we do not fully understand can not only slow down clinical translation, but it can even sour an entire field, hurting reputation and investment.”

As therapeutic platforms become increasingly sophisticated, he believes scientific rigor will become even more important. The sheer amount of data generated, and the intense race to be first to discover, first to patent, and first to market will make it even more challenging.

“Thinking mechanistically and getting it right before we go on to the next step is the classic scientific approach, and it is just as true and necessary today as it was 50 years ago.”

The Breakthroughs He’s Most Proud Of

While Keith expresses pride in all the papers he and his team have published, he’s particularly proud of two papers currently in revision. Both collaborations involved Masad Damha and esteemed colleagues, including P.I. Pradeepkumar and Sergey Korolev. The first, authored by Pater et al., originally aimed to explore the chemical modification of Cas9 CRISPR RNAs over a decade ago. However, the team encountered a significant obstacle, which Keith and Masad dubbed the “2’-hydroxyl barrier,” in which certain positions of the guide RNA’s ribose simply cannot be modified (4).

“We finally cracked the code, at least for some of these positions,” he says. “It would have been easy to give up, since this discovery required deep mechanistic investigations into Cas9 structure-function. But I’m happy we kept going, and I hope it leads to new delivery modalities for CRISPR.”

The second project focused on CRISPR guide RNA architecture, specifically comparing the effect of dual-guide versus single-guide RNAs on Cas9 activity and specificity. This endeavor proved more complex than anticipated, requiring several years of work to elucidate the mechanism. Ultimately, both projects resulted in breakthroughs.

“Stories like that, where we did not give up, are the ones I’m most proud of,” he says.

In addition to his publications, Gagnon has received numerous honors, including the OTS Young Investigator Award (2017). He has served on the OTS Board of Directors and continues to contribute through its Scientific Advisory Board.

The Mentors, Trainees, and Collaborators Who Shaped His Career

Dr. Maxwell and Dr. Corey were key mentors in Keith’s education and career. In his first independent faculty position, Ramesh Gupta, PhD, whom he describes as a wonderful department chair, also served as a mentor, sharing tips and tricks for focusing his research and navigating administrative duties, while being a true friend.

“I would say having people that inspire you, believe in you, and give you a chance can make all the difference,” he says.

Today, Keith strives to provide the same support to his trainees.

“I take their training and success very seriously. It starts with principles of how to approach problems, how to design experiments, and how to work with and treat others fairly. Things that will help them no matter where they go in life.”

Among his closest collaborators is Masad Damha, whom Keith affectionately describes as a “partner in crime.” He notes that Damha has indirectly mentored him through their shared love for exciting nucleic acid chemistry and biochemistry. Other influential collaborators include P.I. Pradeepkumar, an expert nucleic acid chemist doing great MD simulation work, Sergey Korolev, for all his help with structural studies, and Joao Mamede, who has helped Keith’s lab break into a new area of viral RNA epitranscriptomics.

“Having peers like this is wonderful,” he says. “They have shown me great patience and camaraderie.”

For young scientists considering careers in the field, his advice is simple: “Don’t give up easily. Find out what it is that you can be great at and go for it. Don’t be enamored by self-promotion, big paychecks, or fame. First, focus on training yourself to do world-class science and be a critical problem solver. Everything else will follow.”

Life Beyond the Lab

Despite his passion for science, Keith reminds himself there is more to life than science. “Kids grow up whether you are paying attention or not. And T-I-M-E is how they spell the word love. Spend the time, laugh, and forget about the cares of the world sometimes.”

Learning to accomplish more in less time, accepting that tomorrow is another day, and relying on a supportive spouse when deadlines become unavoidable have all helped him maintain balance. Remembering that saying yes to one thing means you will probably have to say no to something else, trying not to make promises that can’t be kept, and communicating clearly when obligations can’t be met are also key.

He also believes in protecting core principles. “It is important to find and hold values and principles greater than yourself that can guide your vision. Despite the pressures, you can never compromise on your core principles, in family, life, and science.” For Keith, those principles became clearer when he found Jesus during college, a decision he says unfailingly continues to guide him today.

Outside the laboratory, he enjoys volunteering in the community, spending time supporting his children’s sports and school activities, and working with his hands, which at this stage of life includes home improvement projects and fixing cars.

Legacy and Looking Ahead

Asked how he would like to be remembered, Keith’s answer reflects both his scientific ambitions and his personal values.

Professionally, he hopes to be remembered for a breakthrough that originated in his laboratory, which may be yet to come. Personally, he hopes colleagues and trainees remember him as someone who valued research creativity and quality and was generous in sharing his experiences and resources with other scientists.

“In simplistic terms, if I could help cure a disease, discover a new pathway or mechanism, and see my trainees go on to be successful, I would be quite happy.”

To stay up to date with Keith’s latest research and contributions, visit www.labgagnon.com or search BioRxiv and PubMed for new releases from his research group. To read key journal articles on his work, find a list of some of Keith’s various publications below.

Research Contributions:

1. Bleichert F, Gagnon KT, Brown BA 2nd, Maxwell ES, Leschziner AE, Unger VM, Baserga SJ. A dimeric structure for archaeal box C/D small ribonucleoproteins. Science. 2009 Sep 11;325(5946):1384-7. doi: 10.1126/science. 1176099. PMID: 19745151; PMCID: PMC2975540.
2. Gagnon KT, Pendergraff HM, Deleavey GF, Swayze EE, Potier P, Randolph J, Roesch EB, Chattopadhyaya J, Damha MJ, Bennett CF, Montaillier C, Lemaitre M, Corey DR. Allele-selective inhibition of mutant huntingtin expression with antisense oligonucleotides targeting the expanded CAG repeat. Biochemistry. 2010 Nov 30;49(47):10166-78. doi: 10.1021/bi101208k. Epub 2010 Nov 8. PMID: 21028906; PMCID: PMC2991413.
3. Gagnon KT, Li L, Chu Y, Janowski BA, Corey DR. RNAi factors are present and active in human cell nuclei. Cell Rep. 2014 Jan 16;6(1):211-21. doi: 10.1016/j.celrep.2013.12.013. Epub 2014 Jan 2. PMID: 24388755; PMCID: PMC3916906.
4. Pater AA, Barber HM, Sudhakar S, Chilamkurthy R, Jana SK, Parasrampuria MA, Bosmeny MS, Graczyk-Marrs JA, Eddington SB, Blazier CA, Abdullahu L, Malek-Adamian E, Barkau CL, O’Reilly D, Korolev S, Pradeepkumar PI, Damha MJ, Gagnon KT. Chemical control of 2′-hydroxyl-dependent Cas9 target engagement enables CRISPR RNA ribose replacement. bioRxiv [Preprint]. 2026 Jan 26:2026.01.26.701763. doi: 10.64898/2026.01.26.701763. PMID: 41659633; PMCID: PMC12874002.
5. Barkau CL, O’Reilly D, Rohilla KJ, Damha MJ, Gagnon KT. Rationally Designed Anti-CRISPR Nucleic Acid Inhibitors of CRISPR-Cas9. Nucleic Acid Ther. 2019 Jun;29(3):136-147. doi: 10.1089/nat.2018.0758. Epub 2019 Apr 16. PMID: 30990769; PMCID: PMC6555185.
6. Ageely EA, Chilamkurthy R, Jana S, Abdullahu L, O’Reilly D, Jensik PJ, Damha MJ, Gagnon KT. Gene editing with CRISPR-Cas12a guides possessing ribose-modified pseudoknot handles. Nat Commun. 2021 Nov 15;12(1):6591. doi: 10.1038/s41467-021-26989-z. PMID: 34782635; PMCID: PMC8593028.
7. Bosmeny MS, Pater AA, Zhang L, Larkai LL, Sha BE, Lyu Z, Damha MJ, Mamede JI, Gagnon KT. A nanopore-based HIV-1 reference epitranscriptome. Nucleic Acids Res. 2026 Mar 19;54(6):gkag220. doi: 10.1093/nar/gkag220. PMID: 41854072; PMCID: PMC13000461.

Antisense oligonucleotides (ASOs) have emerged as promising drug candidates for the treatment of genetic diseases. Because of their ability to target virtually any disease-related gene product, several ASO drugs have been approved, and many more are in development (1). While they remain among the most precise therapies, investigations are ongoing to find improvements and increase safety. A recent study from Karolinska Institutet published in Nature Communications found that ASOs can activate a cell’s DNA damage response even when no damage is present.

Background: chemistry and cellular behavior of ASOs

Most ASO therapeutics are chemically modified to include phosphorothioate (PS) backbone modifications, which improve their stability, cellular uptake, potency, and tissue delivery (2). Importantly, the PS modification also increases protein binding (2). Previous studies have shown that specific protein binding influences the localization of PS ASOs within the cell (3). These proteins can direct ASOs to specific cellular compartments, including the nucleus, where DNA repair proteins reside, as well as stress granules and paraspeckles, where they can accumulate and interfere with normal cellular processes (1, 3).

A 1998 study provided evidence that PS-modified ASOs can form abnormal nuclear structures by trapping proteins, regardless of their intended target (4). This helps explain that the PS bodies identified in the new study are a specific type that go a step further by mimicking DNA damage and activating repair pathways.

The discovery: ASOs and DNA repair disruption

Against this background, Marianne Farnebo and her team set out to better understand how ASOs might be influencing DNA repair. Farnebo, the research group leader at the Department of Oncology-Pathology at Karolinska Institutet and the senior author of the study, investigates the role of endogenous RNA in DNA repair. They previously found that RNA can bind to DNA repair enzymes and modulate their catalytic activity (5). Farnebo and her team often use ASOs to knock down RNAs of interest to study their functions. During these experiments, they noticed that their control ASOs unexpectedly affected DNA repair, making it difficult to distinguish specific effects from nonspecific ones. To continue using ASOs reliably, they needed to understand and resolve this issue.

Farnebo explained that synthetic ASOs, which closely resemble natural RNA as negatively charged, single-stranded nucleic acid polymers, can also bind to DNA repair enzymes and dysregulate their activity, suggesting that ASOs can mimic endogenous RNA and thereby modulate DNA repair pathways. The researchers found that when ASO molecules bind to DNA repair proteins, they form dense clusters called PS bodies inside the cell’s nucleus. These clusters attract and trap DNA repair proteins, activating a false DNA damage response. This disrupts the natural repair process and, over time, causes real DNA damage.

“Our results show that ASOs can trigger a repair response that should not normally be activated, and this affects the cell’s normal handling of DNA damage,” said Farnebo in the news release.

Mechanism: phase separation and protein activation

To understand how these clusters form and why they activate repair enzymes, the researchers examined their physical properties. They found that these structures behave like liquid droplets, in a process known as phase separation where molecules can condense into dense, dynamic compartments. This environment can concentrate proteins and alter their activity, effectively switching on DNA repair enzymes (such as DNA-PKcs, ATM, and PARP1) simply by bringing them together, even in the absence of damaged DNA (1).

Previous studies have also demonstrated that ASO-protein aggregates can undergo liquid-to-solid phase transitions. In one such study, researchers found that while some aggregates form with both nontoxic and toxic ASOs, toxic ASOs can also form unique nucleolar aggregates associated with dysfunction and cell death (6).

The role of the PS backbone

Farnebo and her team’s findings point to the importance of the chemical properties of ASOs themselves. The study found that both DNA- and RNA-based ASOs with a phosphorothioate (PS) backbone can induce PS body formation in cells, suggesting that this chemical feature alone is sufficient to drive clustering. This raises the possibility that similar interactions, if present naturally, could aid in the formation of droplet-like clusters of DNA repair proteins (1).

Nuclear organization and protective mechanisms

Interestingly, however, ASOs do not behave uniformly across all regions of the nucleus. “We find that ASOs are not enriched at DNA break sites, but instead excluded, even though the concentration of repair factors is high at these sites,” the authors stated (1). This exclusion may serve as a protective mechanism to prevent disruption of critical repair processes (1).

Together, these findings suggest that ASOs can influence nuclear organization and cellular function in multiple ways. Similar effects have been reported in other studies, where fully PS-modified oligonucleotides were shown to induce structured nuclear inclusions, redistribute nuclear proteins, and alter gene expression patterns (7). The work by Farnebo and colleagues suggests that when such reorganization involves DNA repair proteins, it may lead to inappropriate activation of DNA damage signaling pathways.

Clinical context and emerging risks

These findings raise important questions about how ASOs behave under clinically relevant conditions. Farnebo noted that it is important to distinguish between the ASO treatment used in the study and clinically used methods, in which significantly lower concentrations of ASOs reach the cell nucleus. Importantly, she said their in vivo data indicate that ASOs can activate DNA damage signaling even at lower, clinically relevant concentrations (1).

Doctoral student and first author Linn Hjelmgren explained, “Our results show that the impact on DNA repair can occur in several distinct ways, not just through the clusters formed in the cell nucleus.” The authors pointed to several possible pathways, including direct interactions with repair enzymes and broader transcriptional changes induced by ASO treatment (1).

“With ongoing clinical use and the rapid development of ASO-based drugs – especially those designed to enhance cellular uptake and bypass endosomal trapping – the potential risk of interfering with DNA repair is likely to grow,” she explained. “This underscores the need to communicate these findings broadly within both the RNA therapeutics field and the pharmaceutical industry.”

Broader implications for biology and therapeutics

According to Farnebo, the realization that synthetic oligonucleotides can mimic endogenous RNA and affect RNA-dependent processes has broad implications for both basic research and therapeutic applications.

“Our demonstration that ASOs can strongly activate DNA damage signaling and suppress DNA repair reveals a previously unrecognized mechanism of ASO-induced toxicity,” she explained.

“These findings advance the fundamental understanding of RNA-mediated DNA repair and are highly relevant for the safety assessment and future development of RNA-based therapeutics,” said Farnebo.

Future directions

Farnebo and her team hope the field will further investigate how synthetic oligonucleotides interact with DNA repair pathways, and that future design and safety testing of next-generation RNA therapeutics take this into consideration.

“A key open question is how ASOs influence DNA repair in vivo, particularly across different tissues and delivery methods,” said Farnebo. “This is essential for a thorough safety evaluation.”

The researchers are continuing their work by examining ASO-induced dysregulation of DNA repair in vivo using mouse models, including multi-organ analysis following treatment with fluorescent ASOs. Their future work will focus on identifying strategies to prevent or mitigate ASO-driven effects on DNA repair.

Farnebo said collaborations enabled the team to evaluate ASO effects in an ASO-treated mouse model, in which they observed activation of the DNA damage response in cells with high ASO uptake. Although she said these findings should be validated in larger cohorts, they provide in vivo proof-of-principle that ASOs can influence DNA repair under clinically relevant delivery conditions. “These findings suggest that ASOs can mimic natural RNA and alter RNA-dependent DNA repair functions, potentially contributing to unintended therapeutic side effects.”

Despite these findings, ASOs remain a powerful and clinically validated therapeutic platform. Their ability to precisely target disease-causing genes has transformed treatment options for several rare conditions. However, as newer ASO therapies are designed to improve cellular uptake and increase nuclear delivery, the potential for interference with DNA repair may also rise. Given the growing clinical use of ASOs, these findings highlight the importance of carefully evaluating their effects on genome stability (1).

References:

1. Hjelmgren, L., Zhou, Q., Schmidli, S. et al. Dysregulation of the DNA damage response by phosphorothioate antisense oligonucleotides. Nat Commun 17, 2111 (2026). https://doi.org/10.1038/s41467-026-69980-2
2. Crooke ST, Vickers TA, Liang XH. Phosphorothioate modified oligonucleotide–protein interactions. Nucleic Acids Research. 2020;48(10):5235–5253. doi:10.1093/nar/gkaa299.
3. Bailey JK, Shen W, Liang XH, Crooke ST. Nucleic acid binding proteins affect the subcellular distribution of phosphorothioate antisense oligonucleotides. Nucleic Acids Research. 2017;45(18):10649–10671. doi:10.1093/nar/gkx709.
4. Lorenz P, Baker BF, Bennett CF, Spector DL. Phosphorothioate antisense oligonucleotides induce the formation of nuclear bodies. Mol Biol Cell. 1998 May;9(5):1007-23. doi: 10.1091/mbc.9.5.1007. PMID: 9571236; PMCID: PMC25326.
5. Bergstrand S, O’Brien EM, Coucoravas C, Hrossova D, Peirasmaki D, Schmidli S, Dhanjal S, Pederiva C, Siggens L, Mortusewicz O, O’Rourke JJ, Farnebo M. Small Cajal body-associated RNA 2 (scaRNA2) regulates DNA repair pathway choice by inhibiting DNA-PK. Nat Commun. 2022 Feb 23;13(1):1015. doi: 10.1038/s41467-022-28646-5. PMID: 35197472; PMCID: PMC8866460.
6. Liang XH et al. Solid-Phase Separation of Toxic Phosphorothioate Antisense Oligonucleotide-Protein Nucleolar Aggregates Is Cytoprotective. Nucleic Acid Therapeutics. 2021;31(2):67–80.
7. Flynn LL et al. Single stranded fully modified-phosphorothioate oligonucleotides can induce structured nuclear inclusions, alter nuclear protein localization and disturb the transcriptome in vitro. Frontiers in Genetics. 2022;13:791416. doi:10.3389/fgene.2022.791416.

“The views, opinions, findings, and conclusions or recommendations expressed in these articles and highlights are strictly those of the author(s) and do not necessarily reflect the views of the Oligonucleotide Therapeutics Society (OTS). OTS takes no responsibility for any errors or omissions in, or for the correctness of, the information contained in these articles. The content of these articles is for the sole purpose of being informative. The content is not and should not be used or relied upon as medical, legal, financial, or other advice. Nothing contained on OTS websites or published articles/highlights is intended by OTS or its employees, affiliates, or information providers to be instructional for medical diagnosis or treatment. It should not be used in place of a visit, call, consultation, or the advice of your physician or other qualified health care provider. Always seek the advice of your physician or qualified health care provider promptly if you have any healthcare-related questions. You should never disregard medical advice or delay in seeking it because of something you have read on OTS or an affiliated site.”

In November, Food and Drug Administration (FDA) officials introduced the Plausible Mechanism Pathway, a regulatory tool designed to make it easier to approve treatments — specifically investigational gene therapies — for rare conditions.

An article published in The New England Journal of Medicine (1) discussed the successful treatment of KJ Muldoon, a baby born with a rare, life-threatening liver disorder and a pathway for approval of treatments for rare diseases. This was followed by the release of the FDA’s Draft Guidance for the Plausible Mechanism Pathway in February 2026. KJ received a bespoke gene-editing therapy within six months, demonstrating the value of individualized therapies and prompting the FDA to create a new pathway. For rare diseases, the population size is often too small to conduct randomized trials, but the plausible mechanism pathway helps overcome this barrier by considering a disease’s underlying pathway and a therapy’s mechanism of action (1).

For gene editing companies, this could mean they could use data from an initial approval to make modifications and customize the therapy for another patient with a slightly different mutation, provided it meets the plausible mechanism pathway requirements. For patients with rare diseases, this approach could eliminate the need to wait years for treatment, and companies like Aurora Therapeutics plan to make that happen.

Origins of Aurora Therapeutics

It was only two years ago that Fyodor Urnov, a professor at the University of California, Berkeley, was lecturing and writing about CRISPR’s potential to treat patients with ultra-rare mutations — the barrier was not the technology, but rather companies choosing to develop these bespoke therapies and regulators approving them. Johnny Hu, a venture capitalist at Menlo Ventures with a Ph.D. in gene editing, wanted to help.

Both Urnov and Hu knew the technology was possible, but what was less certain was building a company that would actually succeed. With $16 million in seed funding from Menlo Ventures, Urnov joined forces with Nobel laureate and co-inventor of CRISPR technology, Jennifer Doudna, and formed Aurora Therapeutics.

The 11-person startup launched in January with a mission to use CRISPR to develop gene-editing treatments for patients with both rare and common mutations. They hope to start a trial in 2027.

Impact of the New FDA Pathway on Aurora and other gene therapies

In the past, existing companies have shied away from developing personalized treatments, notes Aurora’s leadership; however, with the success of KJ’s treatment and the new FDA pathway, a new interest has emerged. The Aurora team credits the new plausible mechanism pathway, as well as more efficient personalization and manufacturing of editors, as making startups like theirs possible.

According to the company’s recent press release, a key component of its model is the emerging regulatory changes that support grouping multiple mutations within a disease into unified developmental paths, which it said could make personalized therapies economically and operationally viable.

“You can keep over 99% of the drug the same and then retarget it to each individual mutation,” Hu says. While some aspects of the drugs will differ by patient, Aurora plans to use the FDA’s new plausible mechanism pathway to obtain approval for the platform as a whole.

Aurora will also use artificial intelligence to design its highly personalized CRISPR-based editors for rare genetic diseases.

“Since its discovery, CRISPR has offered the promise of treating the root causes of genetic disease, but we lacked a scalable way to bring those therapies to patients with rare mutations,” said Aurora co-founder Jennifer Doudna, Ph.D. “By innovating in both clinical development and approval pathways, Aurora could help address the hurdles of providing gene editing therapies for patients who were previously out of reach.”

While Aurora credits the pathway with making personalized therapies economically viable by reusing most of the drug and retargeting only the guide RNA, manufacturing and quality standards for individualized products remain stringent, potentially limiting scalability for academic or non-profit efforts. Additionally, personalized therapies often face high production costs and complex chemistry, manufacturing, and control requirements, which could strain small developers or limit access.

Another concern lies in recent FDA decisions on experimental drugs for rare conditions, which have created uncertainty and doubts about whether the agency will consistently apply the promised flexibilities of the pathway. Therapies for Duchenne muscular dystrophy, Spinocerebellar Ataxia, Mucopolysaccharidosis II, and Epstein-Barr virus–positive post-transplant lymphoproliferative disease have all received letters denying their approval. Also notable is the rejection of uniQure’s Huntington’s disease therapy, in which the agency required more rigorous data than expected, publicly challenged the program, and a senior FDA official anonymously questioned whether there was any therapeutic benefit. These developments have strained the FDA’s relationship with the rare disease community and left companies and researchers questioning how consistently and predictably the FDA will apply this new regulatory approach.

Aurora’s Lead Program: Phenylketonuria (PKU)

Aurora’s lead program focuses on phenylketonuria (PKU), a rare liver disorder caused by mutations in the PAH gene that lead to a toxic buildup of phenylalanine in the blood. If not caught early and treated with a special diet, the disease can cause impaired brain development in children and teens. Though there are over 1,600 known PKU mutations, Aurora will start by addressing the three most common variants and expand from there, while also pursuing other genetic liver diseases.

Because PKU is well-understood biologically and has already been a target of genetic medicine, Aurora CEO Edward Kaye believes the disease perfectly fits the plausible mechanism pathway.

“We understand the proximate cause of the disease, and we know how to address it,” he said. Additionally, the disease has a high unmet need, with an estimated 13,800 individuals living in the United States with PKU as of 2026.

Aurora won’t be the only company looking to treat the rare metabolic disease. Kiran Musunuru and Rebecca Ahrens-Nicklas, two of the lead scientists behind Baby KJ’s treatment, have a similar blueprint for PKU. While the pair is now working on urea cycle disorders — the type of rare disease KJ has — they have licensed the PKU mouse models they built to several companies. Musunuru says if PKU ends up being the next disease companies pursue, he’s happy to have sparked interest from his academic work.

It’s worth noting that gene editing is not without risks, including the possibilities of off-target effects, immune responses, and unknown durability. KJ’s treatment, while successful thus far, is not considered a cure and will require lifelong monitoring. Additionally, the pathway is a draft guidance, not a guaranteed fast-track, with the FDA emphasizing that the evidence must still rule out natural variability or placebo effects. Recent FDA decisions, such as its rejection of uniQure’s Huntington’s disease drug, highlight the tension between the rhetoric of flexibility and demands for robust data.

Families and Foundations Driving Custom Genetic Treatments

Aurora joins other organizations working in the rare disease space that use CRISPR and other gene-editing technologies. The n-Lorem Foundation, a nonprofit organization, was founded by Dr. Stanley Crooke and provides experimental antisense oligonucleotide (ASO) based treatment to patients with ultra-rare diseases. As of the start of 2026, n-Lorem’s ASOs are treating more than 50 patients.

ASO technology has also continued to evolve in the N-of-1 space, with n-Lorem’s current portfolio including several allele-specific RNase H1 ASO programs, reflecting the growing importance of this approach in personalized medicine. According to the organization, many nano-rare patients carry gain-of-function mutations that can be addressed through RNase H1 technologies. In many cases, patients require an allele-selective RNase H1 strategy to preserve the function of the wild-type mRNA while degrading mutant mRNA. These strategies require extensive screening, optimization, and expertise to identify an optimized ASO for an individual patient.

While achieving this level of selectivity remains a significant challenge, recent studies have explored strategies to improve allele-specific RNA targeting, including optimizing gapmer ASO design parameters,such as mixmer ASO design and introducing mismatched nucleotides (3).  Researchers have also developed engineered RNA-cleaving DNAzymes capable of allele-specific knockdown while minimizing RNase H1-mediated cleavage (4). Together, these approaches highlight ongoing efforts to improve the precision of oligonucleotide therapeutics for patients who require selective targeting of disease-causing variants while preserving expression of the normal allele.

The Valeria Association, named after Valeria Schenkel, who was born in 2018 with an ultra-rare mutation in the KCNT1 gene, collaborated with researchers from Harvard and Yale to create Valeriasen — an individualized ASO therapy — which was given to Valeria in 2020. Sadly, the little girl passed away in 2021, but the non-profit continues to work on accelerating the research, development, and implementation of individualized therapies for children with ultra-rare genetic diseases, specifically targeting neurodevelopmental disorders like KCNT1-related epilepsy. The KCNT1 Epilepsy Foundation is another non-profit with a similar goal of speeding up research into KCNT1-related epilepsy and supporting families affected by the disease.

Mila’s Miracle Foundation, named after the first person — a little girl — to receive a bespoke therapy, has the mission to find and fund paths to cure devastating neurological conditions and to help grow the emerging field of individualized medicines. Mila’s individualized medicine, called Milasen, was an ASO treatment targeting the mutation causing her Batten’s disease. Like many children with rare diseases, Mila has passed away, but the Foundation continues to work on making an impactful treatment platform.

Also rising from Mila’s experience, the N=1 Collaborative was launched in 2021 as the first international hub, comprising a network of experts, doctors, researchers, patients, and companies working together to bring individualized treatments to patients with rare diseases. The organizing committee includes scientific leaders from around the world, such as Dr. Tim Yu, the designer of milasen, and Julia Vitarello, Mila’s mother. The N=1 Collaborative and its hundreds of participants are dedicated to guiding this rapidly developing new branch of medicine

Cure Rare Disease, another nonprofit, was similarly inspired by family members seeking a cure for their child. In this case, it was Terry, who was diagnosed with Duchenne muscular dystrophy (DMD) at three years old. A treatment was created, but Terry did not live to see it. Terry’s brother, Rich Horgan, however, continues to advocate for the development of genetic therapy for rare diseases.

“There are hundreds of thousands of Terrys waiting for their chance to hit back. His legacy is a future where no family has to hear, ‘There’s nothing we can do,’” says Horgan.

The Future of Rare Disease Therapies

There are many other Valerias, Milas, and KJs, too, because, as Hu explains, even though each individual disease is rare, combined, there are hundreds of millions of rare-disease patients. In the U.S. and Canada alone, 37 million people have a rare disease. However, while collectively large, each individual condition is a small market, raising questions about pricing, reimbursement, and whether the for-profit models will truly serve the highly rare diseases that nonprofits target. Current gene therapies often cost $1–3+ million per patient, creating barriers for patients, insurers, and global health systems and potentially exacerbating inequities, especially if overwhelming application volume strains resources. As with Baby KJ, some treatments may require lifelong surveillance, further driving costs and stretching resources.

The emergence of the FDA’s plausible mechanism pathway, together with advances in CRISPR, ASO technologies, and artificial intelligence, represents a potential step forward for patients with ultra-rare diseases, though challenges remain. Companies like Aurora Therapeutics and nonprofits such as n-Lorem, N=1 Collaborative, Mila’s Miracle Foundation, the Valeria Association, the KCNT1 Epilepsy Foundation, and Cure Rare Disease are translating individual tragedies into collective progress, building models that could make bespoke therapies more feasible and widely available. While not every story will have the outcome that families hope for, each effort brings the field closer to a future in which “too rare” is no longer a barrier to treatment. However, significant barriers, including safety, cost, equity, and regulatory consistency, must be addressed for these bespoke therapies to benefit more than a privileged few.

References:

1. Prasad V, Makary MA. FDA’s New Plausible Mechanism Pathway. N Engl J Med. 2025 Dec 11;393(23):2365-2367. doi: 10.1056/NEJMsb2512695. Epub 2025 Nov 12. PMID: 41223362.
2. FDA Draft Guidance: Considerations for the use of the Plausible Mechanism Framework to Develop Individualized Therapies that Target Specific Genetic Conditions with Known Biological Cause. 2026 Feb 25.
3. Aguti S, Cheng S, Ala P, Briggs S, Muntoni F, Zhou H. Strategies to improve the design of gapmer antisense oligonucleotide on allele-specific silencing. Mol Ther Nucleic Acids. 2024 Jun 5;35(3):102237. doi: 10.1016/j.omtn.2024.102237. PMID: 38993932; PMCID: PMC11238192.
4. Erica M Lee, Kim Nguyen, Noah A Setterholm, Turnee N Malik, John C Chaput, Allele-specific knockdown by an engineered DNAzyme capable of RNase H1 evasion, Nucleic Acids Research, Volume 54, Issue 1, 13 January 2026, gkaf1476, https://doi.org/10.1093/nar/gkaf1476

“The views, opinions, findings, and conclusions or recommendations expressed in these articles and highlights are strictly those of the author(s) and do not necessarily reflect the views of the Oligonucleotide Therapeutics Society (OTS). OTS takes no responsibility for any errors or omissions in, or for the correctness of, the information contained in these articles. The content of these articles is for the sole purpose of being informative. The content is not and should not be used or relied upon as medical, legal, financial, or other advice. Nothing contained on OTS websites or published articles/highlights is intended by OTS or its employees, affiliates, or information providers to be instructional for medical diagnosis or treatment. It should not be used in place of a visit, call, consultation, or the advice of your physician or other qualified health care provider. Always seek the advice of your physician or qualified health care provider promptly if you have any healthcare-related questions. You should never disregard medical advice or delay in seeking it because of something you have read on OTS or an affiliated site.”

Date: May 21, 2026
Time: 11-12pm EDT / 5-6pm CEST

Title: Bioanalysis of Oligonucleotide Therapeutics via Nucleic Acid Nanorobotic Platform

Description:

Dynamic DNA nanotechnology enables the isothermal and enzyme-free exchange of nucleic acid strands. The underlying mechanism of action in this field is known as toehold-mediated strand displacement. Recently, dynamic DNA nanotechnology has been applied in bioanalysis of oligonucleotide therapeutics. In this webinar the principles behind nucleic acid nanorobotics will be described. Followed by two recently published case studies demonstrating (1) accuracy and precision in ASO quantification direct to mouse plasma and (2) quantification of ASO-small molecules conjugates in plasma and liver tissue pharmacokinetic studies.

Speaker:

Intellia Therapeutics recently announced that the U.S. Food and Drug Administration (FDA) has lifted the hold on its clinical trial for the investigational CRISPR-based gene-editing therapy, nexiguran ziclumeran, also known as nex-z or NTLA-2001.

The four-month hold was implemented after a patient in the MAGNITUDE study experienced severe liver toxicity, specifically elevated liver transaminases and increased total bilirubin, in a patient who had received a dose of nex-z. The patient died following hospitalization, which Intellia attributes to complicating comorbidities and not just the therapy. A hold was also placed on the related MAGNITUDE-2 Phase 3 trial, which was lifted in late January.

The MAGNITUDE study is testing a research medicine to help people with transthyretin amyloidosis, also called ATTR, a rapidly progressive and ultimately fatal disease caused by misfolded transthyretin proteins. Specifically, MAGNITUDE is designed for ATTR-CM, a heart-related form of transthyretin amyloidosis, while MAGNITUDE-2 is for hereditary transthyretin amyloidosis (ATTRv-PN) with polyneuropathy, a nerve-related form. Both are multinational, double-blind, placebo-controlled trials with treatment consisting of a single 55mg intravenous infusion of nex-z or placebo. Patients between the ages of 18 and 90 are eligible for the MAGNITUDE study if they’ve been diagnosed with heart failure due to ATTR and have experienced it in the past year; women are eligible if they can no longer have children.

At the time of the hold, over 650 patients were enrolled in MAGNITUDE and 47 in MAGNITUDE-2, with over 450 of these patients estimated to have already been dosed with nex-z. The FDA’s lifting of the hold on the MAGNITUDE trials comes after Intellia agreed to several safety measures, including enhanced monitoring of liver laboratory tests; guidance on short-term steroid treatment if liver enzymes are elevated shortly after dosing; and exclusion of patients with certain liver issues, and those with a recent history of cardiovascular instability.

“We are very pleased to have aligned with the FDA on the path forward for our Magnitude clinical trial, with measures designed to further enhance patient safety and allow us to continue to investigate nex-z in a broad ATTR-CM population,” Intellia President and CEO John Leonard, M.D., said in the press release.

Following the lifts, Leonard states that Intellia, in partnership with Regeneron, is now focused on completing enrollment in both ongoing trials.

Analysts from Evercore ISI say the safety adjustments are modest and that the hold was lifted relatively quickly, likely causing little disruption to the clinical timeline. The regulatory developments are significant given nex-z’s potential to provide a one-time treatment for such a devastating disease.

Transthyretin amyloidosis (ATTR): a progressive and often fatal disease

Transthyretin amyloidosis (ATTR) is caused by misfolded transthyretin proteins. As these proteins break down into amyloid fibrils and accumulate in organs, they can cause irreversible damage and lead to premature death. When amyloid deposits amass in the heart, the walls can become stiff and cause cardiomyopathy, a condition that makes it difficult for the heart to pump blood. As the disease progresses, eventually the heart is unable to adequately do its job and heart failure occurs.

Patients with Transthyretin amyloidosis (ATTR) have a median survival rate of two to six years after diagnosis. Unfortunately, most patients remain undiagnosed and untreated while experiencing symptoms that mimic other conditions, like heart failure caused by high blood pressure, hypertension, or hypertrophic cardiomyopathy. Other symptoms can include shortness of breath even while resting or with little exertion, lower extremity swelling, increased heart rate, abnormal heart rhythms, confusion or difficulty thinking, carpal tunnel syndrome and pain and numbness in the hands and feet, known as peripheral neuropathy.

However, ATTR does not affect all patients in the same way, and the disease can be put into two major categories: hereditary ATTR-CM (hATTR), which affects approximately 50,000 people worldwide, and wild-type ATTR-CM (wtATTR), which affects approximately 200,000 to 300,000 people worldwide. In hereditary ATTR-CM, a mutation in the transthyretin gene can cause amyloid deposits in the heart, nerves, and potentially other organs. Symptoms usually appear later in life but can start as early as 30. Wild-type ATTR-CM occurs without a transthyretin gene mutation and does not run in families, typically presenting much later in life.

Given the progressive and often fatal nature of ATTR, nex-z aims to address the disease by targeting the root cause: production of the transthyretin protein.

Nexiguran ziclumeran — nex-z: a one-time treatment

Nexiguran ziclumeran (formerly known as NTLA-2001 and now known as nex-z) is an investigational in vivo CRISPR-Cas9-based gene-editing therapy. The drug is designed to help those with ATTR, in which misfolded TTR proteins form amyloid deposits that damage organs — primarily the heart or peripheral nerves. Nex-z uses a lipid nanoparticle platform to deliver CRISPR components that inactivate the TTR gene in the liver, permanently reducing transthyretin (TTR) protein production. The therapy is designed to be a one-time treatment for ATTR-CM and ATTRv-PN and has positive Phase 1 data showing durable TTR reductions of 89-90% maintained at 24 months, as well as stable and improved cardiac biomarkers, and a manageable safety profile.

However, like many gene therapies that act in the liver, nex-z is not the first gene therapy to struggle with liver toxicity concerns. Other pharmaceutical companies that use adeno-associated viruses (AAVs) as vectors rather than lipid nanoparticles have experienced similar issues; for example, uniQure reported in a February press release that two patients receiving an investigational AAV gene therapy for Fabry disease experienced elevations in liver enzymes. Following protocol, the company has halted dosing in the mid- and high-dose groups during further assessment. Both affected patients responded to corticosteroid treatment. Additionally, last year, the FDA limited the label of Sarepta Therapeutics AAV gene therapy, Elevidys, for patients with Duchenne muscular dystrophy (DMD), following three liver-related patient deaths.

While safety remains a central focus for gene therapies, the new safety measures allow the clinical trials of nex-z to continue, and it could potentially enter a rapidly growing competitive field of approved ATTR treatments.

From stabilizers to silencers: the competitive landscape in treating ATTR

The existing landscape for approved ATTR treatments focuses on TTR stabilizers to prevent misfolding or silencers to reduce TTR production. However, both these avenues require ongoing dosing, positioning nex-z’s single-dose approach as a breakthrough, should the Phase 3 trial succeed.

Four oral TTR stabilizers are available for ATTR treatment: diflunisal, tafamidis, tolcapone, and acoramidis, but only two — acoramidis and tafamidis — have international approval (1), while diflunisal and tolcapone are considered off-label treatments. Tafamidis, sold under the brand names Vyndaquel and Vyndamax by Pfizer, and Acoramidis, sold as Attruby by BridgeBio Pharma, work by binding to the TTR protein, stabilizing it and slowing its breakdown into the dangerous amyloid deposits. Since the two Tafamidis therapies were approved by the FDA in 2019, the drugs have shown success in reducing mortality and hospitalizations. Acoramidis, approved in late 2024, demonstrated strong Phase 3 clinical data.

TTR gene silencers include inotersen, eplontersen, patisiran, and vutrisiran. Eplontersen, also known as Wainua, received FDA approval in December 2023. The drug, developed by Ionis Pharmaceuticals in partnership with AstraZeneca, is a GalNAc conjugated antisense oligonucleotide (ASO) for treating hereditary polyneuropathy TTR (hATTR-PN) and is the only treatment for the disease that can be self-administered once a month via an auto-injector.

Ionis Pharmaceuticals also has inotersen (Tegsedi) on the market, which shares the same nucleotide sequence as eplontersen and was approved by the FDA and the EU in 2018 for the treatment of hATTR-PN. The ASO drug, administered subcutaneously weekly, binds both wild-type and mutant TTR messenger RNA (mRNA), thereby inhibiting TTR protein expression.

Additionally, Alnylam Pharmaceuticals’ Onpattro (patisiran) and Amvuttra (vutrisiran) are approved for the treatment of hATTR. Both drugs are siRNA-based oligonucleotides but differ in their chemical structures. Onpattro, approved in 2018, is an siRNA, encapsulated in a lipid nanoparticle formulation that requires IV administration every three weeks. Amvuttra, approved in 2022, uses an siRNA-GalNAc conjugate with an enhanced stabilization chemistry that, compared to Onpattro, provides greater potency and higher metabolic stability, enabling subcutaneous injection every three months.

These therapies have transformed the field of ATTR treatment, but all require ongoing dosing. Against this competitive and safety-conscious backdrop, the FDA’s decision to lift the clinical hold on Intellia’s MAGNITUDE and MAGNITUDE-2 trials allows Intellia to resume advancing nexiguran ziclumeran toward a potential one-time CRISPR-based treatment for ATTR. While the recent safety concerns underscore the need for vigilant monitoring of liver toxicity, the protocol changes and resumption of dosing suggest regulators remain confident in the program’s potential overall risk-benefit profile. As Intellia and Regeneron work to complete enrollment and generate pivotal Phase 3 data, the results will be closely watched, as they will answer vital questions, including whether the added monitoring will fully prevent liver issues, how well it will work long-term in a broad patient group, and whether there are any off-target effects. As gene editing is permanent, any off-target effects could have lasting consequences. The phase 3 trial results will be critical in determining whether nex-z earns FDA approval. If successful, it will join a competitive market of ATTR therapies, with its one-time treatment offering another option for treating the disease.

References:

1. Judge, D. P. Current available treatment options targeting TTR tetramer stabilization. European Heart Journal Supplements. https://doi.org/10.1093/eurheartjsupp/suag010

“The views, opinions, findings, and conclusions or recommendations expressed in these articles and highlights are strictly those of the author(s) and do not necessarily reflect the views of the Oligonucleotide Therapeutics Society (OTS). OTS takes no responsibility for any errors or omissions in, or for the correctness of, the information contained in these articles. The content of these articles is for the sole purpose of being informative. The content is not and should not be used or relied upon as medical, legal, financial, or other advice. Nothing contained on OTS websites or published articles/highlights is intended by OTS or its employees, affiliates, or information providers to be instructional for medical diagnosis or treatment. It should not be used in place of a visit, call, consultation, or the advice of your physician or other qualified health care provider. Always seek the advice of your physician or qualified health care provider promptly if you have any healthcare-related questions. You should never disregard medical advice or delay in seeking it because of something you have read on OTS or an affiliated site.”

The sometimes twisty, sometimes intuitive, sometimes amazingly elegant hidden logic of the natural world has always fascinated Dr. Timothy Yu. Knowledge we now take for granted — the genetic code, machinery of transcription, or the layered biological logic of developmental patterning — were once completely mysterious. The ability to discover this hidden knowledge and apply it in the real world to help patients has inspired Dr. Yu throughout his career.

Following his north star: education and training

While Tim is now a neurogeneticist at Boston Children’s Hospital and Harvard Medical School, he grew up in San Diego, where his parents pursued careers in medical research. As a kid, he was unaware of much of their work, but when he went to his mother’s clinic at UCSD Medical Center as a teenager, he was struck by what he saw: young children with Leukemia in hospital gowns, attached to IV poles, bald from their chemotherapy. His mother, a typically cheerful pediatric hematologist and oncologist, told him that half of the kids he’d seen wouldn’t make it.

Shocked, he asked, “Isn’t that so depressing? Why in the world do you do this? Her response: “Actually, when I started 20 years ago, we lost 90% of them. So from my perspective, I’m really proud we’re able to save half.”

Tim followed in his parents’ science-shaped footsteps, studying biochemistry and molecular biology at Harvard College, and then neuroscience in graduate school at the University of California, San Francisco. Approaching the completion of his MD-PhD program, he had to decide: spend years in more medical training, or fast-track into basic science?

After a great deal of soul searching, he decided he wanted to pursue work anchored in real-world problems. Rather than choosing science for science’s sake — getting grants, giving talks, publishing important papers — he believed the truest demonstration of understanding a subject was to show you could put your knowledge to good use.

“This felt to me like a north star: seeing an idea implemented in the real world, for some useful practical purpose. For me, it translated to reaffirming my commitment to the physician-scientist route.”

That decision made, he had to choose a specialty for residency. He noticed many of his peers chose their fields based on their personalities.

“A sort of ‘Sorting Hat’ quiz — based on your personality type, and whether it matched the stereotype of what a particular medical subspecialist was supposed to be like? Friendly, good with kids? Pediatrics or family medicine for you. Like dimly lit rooms, microscopes? Radiologist or pathologist. Like to cut? Surgery for you.”

As he reflected on what to choose, he thought of his mother’s words 15 years ago, on that visit to his mother’s clinic. He decided not to choose a field based on how it looked presently, but on where it was headed, what problems needed to be solved, and where he could see the field going over the next 20 years and where, if given the opportunity, he could help take it.

Encountering antisense technology: finicky and satisfyingly mysterious

Tim did his neurology residency at Massachusetts General Hospital and Brigham and Women’s Hospital, followed by a fellowship in neurodevelopmental genetics at Massachusetts General Hospital and Boston Children’s Hospital. He began groundbreaking work in diagnostic personalized medicine, becoming one of the first to use genome-scale sequencing to identify a human disease gene in 2010 (1). In 2013, he published a key study applying exome sequencing to uncover rare genetic causes of Autism spectrum disorder, which highlighted recessive contributions (2). His research group continues to use advanced sequencing and analytics to understand the genetics of autism and other brain development disorders. These tools have also been translated to the hospital, where analyses of rapid-turnaround genomic sequencing are conducted in both the neonatal intensive care unit and the newborn nursery. However, it would be his later work with antisense technology that would change not only his research but also the field of rare diseases.

Before earning his medical degree, Tim first heard of antisense during his undergraduate years at Harvard in the early 1990s, when one of his classmates in the lab next to his was using antisense oligonucleotides to block gene expression in mammalian cell culture.

“As I remember it, the technology was simple in concept, but it seemed annoyingly finicky and mysterious,” he says.

The next time he encountered antisense technology was in graduate school a few years later, and this time he used it to identify his first disease-causing gene in a worm brain. Surfing the C. elegans genome, he had discovered a worm ortholog of an interesting neuronal cytoskeletal protein on chromosome 5, suspiciously close to unc-34, a mapped genetic locus that, when mutated, caused severe miswiring defects in the worm brain. Knocking down this gene by injecting an antisense oligonucleotide phenocopied the unc-34 phenotype, proving that it was the causative gene. But it was his encounter with the technology in 2017 that proved to be the most important, and which would reshape the direction of his research.

Building a framework for the ‘long tail’ of genetic disease

In January 2017, he came across a Facebook post connecting him to a Colorado family whose daughter had a terrible neurodegenerative disease. Their daughter, Mila, had just been diagnosed with Batten disease, a rare and cruelly progressive condition that impacts around 100 children born in the United States every year. Using their expertise in genome sequencing, Tim and his research group identified a tricky mutation that had eluded detection in Mila’s previous clinical workup; this allowed them to confirm her diagnosis and determine that her brother was not at risk for the disease.

“But we also realized that her unusual mutation could, at least in principle, be correctable with an antisense oligonucleotide,” Tim explains. “The only problem was, who could possibly develop such a drug? Her mutation was at that point — and to this day remains — unique to her — an “N=1.”

The team began speaking to everyone they could think of for advice and, in the end, decided they would have to make the therapy themselves. This would be the world’s first individualized ASO drug tailored to a single patient (3), and while Mila eventually passed away from her condition, her bespoke therapy suppressed her seizures and improved her quality of life. Tim says it was also the start of a remarkable odyssey that, over the past eight years, drew him into the OTS community, reshaped the direction of his research group, and been the source and inspiration of some of the most prized personal and professional partnerships with oligo, rare disease, CMC, and regulatory experts across academia, government, the private sector, and beyond.

“Over and over again, I’ve been struck by the generosity of our OTS community, and their willingness to help their fellow colleagues, and maximize the therapeutic potential of this field,” he says.

Tim lists the therapy they created for Mila, called milasen, as a proud achievement. Since then, he and his team have created several other personalized medicines, including atipeksen (4), for a young girl with a genetic disorder called A-T, or ataxia-telangiectasia, which causes severe neurodegeneration and shortens a person’s life span by an average of 25 years, as well as valeriasen, for a young girl named Valeria with a rare and devastating form of epilepsy (5).

“I’m also proud that two of our programs — one for A-T and one for Niemann Pick type C — led to the first patients to be treated with individualized ASOs in Europe and the UK, respectively, in collaboration with Matthis Synofzik of the University of Tubingen, and Haiyan Zhou and Paul Gissen of University College London and GOSH, respectively,” he says.

These therapies, together with programs led by Neil Shneider and Ionis, and Bob Brown and Jon Watts, set the tone for a productive Critical Path Innovation Meeting with the FDA in 2019, Tim says, which led to the release of the first regulatory draft guidelines for the development of individualized drugs in 2021.

“These have in turn cracked open the door for many, many others to apply genetically precise therapeutic technologies to orphan diseases,” he says.

Beyond the lab, Tim is immensely proud of the N=1 Collaborative, which he founded with Mila’s mother, Julia Vitarello, to advance the international effort to develop individualized therapies for rare diseases. Tim says that what started as a small OTS task force (led by Art Krieg, Annemieke Aartsma-Rus, Jon Watts, and Keith Gagnon) has now grown into a vibrant community working together to make individualized therapeutic approaches safe, affordable, and accessible.

“It’s been a privilege to work alongside such generous contributors to build a framework for the ‘long tail’ of genetic disease,” he says.

Future directions of OTS research and advice for young scientists

The creation of the N=1 therapies is a significant development in the field, and last year, the story of baby KJ and the creation of a bespoke therapy for his rare condition brought public awareness of individualized medicine up another notch, says Tim. Additionally, at the end of 2025, the FDA’s announcement of the plausible mechanism pathway (6), as well as a similar announcement by the MHRA (7), reflects a shift in regulatory readiness for individualized medicine, which Tim says is an acknowledgment that “the time is now.”

As new and more effective chemistries and delivery methods roll out, Tim says each has the potential to improve the therapeutic index and unlock the true programmable potential of oligonucleotide drugs. Additionally, Tim says AI can be an essential strategic enabler that helps guide us more efficiently towards the critical physiochemical, molecular biological, and cellular parameters required to develop safe and successful drugs.

“It will never replace experiments entirely, but will likely help us navigate sequence space more efficiently.”

As for young scientists entering the field, Tim’s advice is to work hard, talk to everyone, and cross-train wherever you can because “the most significant advances in science are usually made at the intersection of disciplines.” Additionally, he encourages scientists to embrace ideas that may feel “big, risky, and unlikely to work,” because it is their job as scientists to tackle important problems.

“We try to think problems through from first principles, to explore what’s scientifically, clinically, and ethically possible — and make it happen. But sometimes that takes us into unfamiliar territory. People pause and ask: Wait—can we really do that?” he says. “It’s natural for people to be uncomfortable. You have to think through all of the angles, be careful. Pressure test your ideas with experts. Be willing to be challenged. Then, if you’re convinced, you have to walk others through it to convince them. You have to talk to a lot of people, in their languages.”

Personal life and legacy: no disease is too rare for attention

The work is demanding, but Tim is grateful for his dedicated team, some of whom have been with him for a decade. He also finds equilibrium through his family.

“Having three kids aged 11 through 15 who are smart and sassy is a very effective way of staying grounded,” he says. Cooking, playing the piano, and, when he has the chance, hiking with the kids and using his long lens to photograph birds and wildlife are among his favorite activities outside the lab. “And sports are a fantastic centering activity for me: tennis, badminton, squash, pickleball.”

Asked what one thing he would want to be remembered for, Tim says it would be forging a path for a new field of “interventional genetics”— marrying science, drug development, and responsible medicine — for the benefit of patients, no matter how “rare” their disease. “The oligonucleotide technology that has been developed by the OTS community has an incredibly broad reach — working together, let’s maximize it.”

To stay up to date with Dr. Tim Yu’s latest research and contributions, visit his lab website here and watch the N1C seminars here.

To read the mentioned research articles, see the list below:

1. Yu TW, Mochida GH, Tischfield DJ, Sgaier SK, Flores-Sarnat L, Sergi CM, Topçu M, McDonald MT, Barry BJ, Felie JM, Sunu C, Dobyns WB, Folkerth RD, Barkovich AJ, Walsh CA. Mutations in WDR62, encoding a centrosome-associated protein, cause microcephaly with simplified gyri and abnormal cortical architecture. Nat Genet. 2010 Nov;42(11):1015-20. doi: 10.1038/ng.683. Epub 2010 Oct 3. PMID: 20890278; PMCID: PMC2969850.
2. Yu TW, Chahrour MH, Coulter ME, Jiralerspong S, Okamura-Ikeda K, Ataman B, Schmitz-Abe K, Harmin DA, Adli M, Malik AN, D’Gama AM, Lim ET, Sanders SJ, Mochida GH, Partlow JN, Sunu CM, Felie JM, Rodriguez J, Nasir RH, Ware J, Joseph RM, Hill RS, Kwan BY, Al-Saffar M, Mukaddes NM, Hashmi A, Balkhy S, Gascon GG, Hisama FM, LeClair E, Poduri A, Oner O, Al-Saad S, Al-Awadi SA, Bastaki L, Ben-Omran T, Teebi AS, Al-Gazali L, Eapen V, Stevens CR, Rappaport L, Gabriel SB, Markianos K, State MW, Greenberg ME, Taniguchi H, Braverman NE, Morrow EM, Walsh CA. Using whole-exome sequencing to identify inherited causes of autism. Neuron. 2013 Jan 23;77(2):259-73. doi: 10.1016/j.neuron.2012.11.002. PMID: 23352163; PMCID: PMC3694430.
3. Kim J, Hu C, Moufawad El Achkar C, Black LE, Douville J, Larson A, Pendergast MK, Goldkind SF, Lee EA, Kuniholm A, Soucy A, Vaze J, Belur NR, Fredriksen K, Stojkovska I, Tsytsykova A, Armant M, DiDonato RL, Choi J, Cornelissen L, Pereira LM, Augustine EF, Genetti CA, Dies K, Barton B, Williams L, Goodlett BD, Riley BL, Pasternak A, Berry ER, Pflock KA, Chu S, Reed C, Tyndall K, Agrawal PB, Beggs AH, Grant PE, Urion DK, Snyder RO, Waisbren SE, Poduri A, Park PJ, Patterson A, Biffi A, Mazzulli JR, Bodamer O, Berde CB, Yu TW. Patient-Customized Oligonucleotide Therapy for a Rare Genetic Disease. N Engl J Med. 2019 Oct 24;381(17):1644-1652. doi: 10.1056/NEJMoa1813279. Epub 2019 Oct 9. PMID: 31597037; PMCID: PMC6961983.
4. Kim J, Woo S, de Gusmao CM, Zhao B, Chin DH, DiDonato RL, Nguyen MA, Nakayama T, Hu CA, Soucy A, Kuniholm A, Thornton JK, Riccardi O, Friedman DA, El Achkar CM, Dash Z, Cornelissen L, Donado C, Faour KNW, Bush LW, Suslovitch V, Lentucci C, Park PJ, Lee EA, Patterson A, Philippakis AA, Margus B, Berde CB, Yu TW. A framework for individualized splice-switching oligonucleotide therapy. Nature. 2023 Jul;619(7971):828-836. doi: 10.1038/s41586-023-06277-0. Epub 2023 Jul 12. PMID: 37438524; PMCID: PMC10371869.
5. Nakayama, T., El Achkar, C.M., Burbano, L.E. et al. Antisense oligonucleotide-mediated knockdown therapy in two infants with severe KCNT1 epileptic encephalopathy. Nat Med (2026). https://doi.org/10.1038/s41591-026-04314-9
6. Prasad V, Makary MA. FDA’s New Plausible Mechanism Pathway. N Engl J Med. 2025 Dec 11;393(23):2365-2367. doi: 10.1056/NEJMsb2512695. Epub 2025 Nov 12. PMID: 41223362.
7. Cheerie D, Meserve MM, Beijer D, Kaiwar C, Newton L, Taylor Tavares AL, Verran AS, Sherrill E, Leonard S, Sanders SJ, Blake E, Elkhateeb N, Gandhi A, Liang NSY, Morgan JT, Verwillow A, Verheijen J, Giles A, Williams S, Chopra M, Croft L, Dafsari HS, Davidson AE, Friedman J, Gregor A, Haque B, Lechner R, Montgomery KA, Ryten M, Schober E, Siegel G, Sullivan PJ, Whittle EF, Zardetto B, Yu TW, Synofzik M, Aartsma-Rus A, Costain G, Lauffer MC; N=1 Collaborative. Consensus guidelines for assessing eligibility of pathogenic DNA variants for antisense oligonucleotide treatments. Am J Hum Genet. 2025 May 1;112(5):975-983. doi: 10.1016/j.ajhg.2025.02.017. Epub 2025 Mar 25. PMID: 40139194; PMCID: PMC12120168.

Additional Links:

8. Rare therapies and UK regulatory considerations
9. Tim Yu: OTS Pathways for Patient Centered Interventional Genomic Medicine
10. Response to the FDA’s proposed pathway for individualized genetic therapies
11. Julia Vitarello & Timothy Yu – GoldLab Symposium 2019
12. Bold Predictions for Human Genomics by 2030

The clock was ticking as soon as baby KJ was born in the summer of 2024. Within two days of his birth, he was lethargic and struggled to breathe. His blood test results showed elevated ammonia levels, leading to a diagnosis of carbamoyl-phosphate synthetase 1 (CPS1) deficiency. This ultra-rare disease affects around 1 in 1,300,000 individuals, and only half of those born with the disorder will make it beyond early infancy.

As soon as KJ was diagnosed, a team of researchers began developing a bespoke gene editor for him. Within six months, the baby had received two doses of his individualized therapy, and his parents say that every day, he’s showing signs of growing and thriving.

Time was of the essence in creating KJ’s treatment — at five months old, his condition had worsened to the point he was on a list for liver transplantation. Due to this urgency, the Food and Drug Administration (FDA) approved his experimental treatment plan after only one week of review following submission of the Investigational New Drug application.

Now, top officials from the FDA want to make it easier to help future baby KJs. Published in the New England Journal of Medicine, Marty Makary and Vinay Prasad explain a Plausible Mechanism Pathway for approving future personalized gene-editing treatments (1).

Shortly after the NEJM article was published, the FDA released a Draft Guidance Document titled “Considerations for the use of the Plausible Mechanism Framework to Develop Individualized Therapies that Target Specific Genetic Conditions with Known Biological Cause.” The draft guidance provides greater detail and addresses some concerns raised after the release of the NEJM article.

Five aspects of KJ’s therapy: how the Plausible Mechanism Pathway works

Traditional FDA drug approvals emphasize proven safety and efficacy through phased clinical trials with multiple participants. However, for patients with rare diseases that have a bespoke therapy targeting their unique genetic mutation, assembling enough participants for a randomized controlled trial is unfeasible due to small patient pools.

The new pathway outlined in the NEJM article addresses this limitation by allowing approval based on a plausible-mechanism framework that includes mechanistic evidence plus clinical-course interpretation. Makary and Prasad state that Baby KJ’s story highlights several aspects that define the FDA’s plausible mechanism category. First, there was a specific molecular or cellular abnormality, not a broad diagnostic spectrum. Makary and Prasad state that the FDA will reserve the Plausible Mechanism Pathway for diseases like this, for which the biological cause is known, to “safeguard against misapplication to disparate conditions with similar phenotypes” (1).

Secondly, the NEJM paper states that KJ’s therapy was developed to target the underlying biological alterations, and thirdly, that his care team relied on a well-characterized natural history of the disease, both of which support a reliable interpretation of clinical changes.

In mouse models of Baby KJ’s disease, results showed successful editing in 42% of liver cells. This evidence of target editing, demonstrated in cell or animal models, is listed as the fourth eligibility criterion for a therapy to be included in the Plausible Mechanism Pathway (1).

Finally, they state that the patient must show improvement in clinical outcomes or course. Makary and Prasad clarify that for conditions with progressive deterioration, consistent improvements will be viewed positively by the FDA. For conditions characterized by episodic waxing and waning, the FDA will look for prolonged periods of disease remission (1).

“The FDA will consider previous clinical course and, in some cases, will view patients as their own control,” the authors state in the NEJM article. “Clinical data must be strong enough to exclude regression to the mean” (1).

FDA Draft Guidance: Further Developing the Plausible Mechanism Pathway Framework

Following the NEJM article, the FDA released the much more comprehensive Draft Guidance, which “outlines a set of recommendations to help developers of individualized therapies generate sufficient clinical safety and efficacy data to demonstrate that a drug or biological product is safe and effective for the intended use, and that the product can be manufactured to regulatory quality standards.” The data generated under this framework is then used to support approval or licensure of the therapy for a specific indication.

While the NEJM article uses five aspects from the development of Baby KJ’s therapy to show how the framework would be developed, the Guidance Document provides far greater detail in outlining recommendations. In some recommendations, the FDA Guidance departs from the NEJM article.

Notably, the Guidance explains that approval occurs within existing regulatory approval pathways. Highlighting this, the Guidance references many prior guidance documents to point to existing recommendations, such as those providing recommendations for design of nonclinical POC and safety studies for genome editing (GE) and antisense oligonucleotide (ASO) products, nonclinical recommendations to assess safety of ASOs, ethical considerations for individualized therapies, development of drugs for rare diseases, IND submissions for individualized RNA-targeted therapies, and potency assays for GE products.

The five aspects mentioned in the NEJM article are clearly provided in the FDA Guidance:

“Application of the plausible mechanism framework involves:

• Identifying a specific genetic, cellular, or molecular abnormality with a clear connection between specific alteration and disease indication
• Developing a therapy that targets the underlying or proximate pathogenic biological alterations
• Relying on a well-characterized natural history of the disease in an untreated population
• Confirming that the target was successfully drugged or edited or both
• Demonstrating improvement in clinical outcomes or course.”

The Guidance specifically discusses genetically targeted therapies, including both GE technologies and RNA-targeted therapies, such as ASOs and small interfering RNAs. However, it also allows that the general concepts may apply to other types of individualized therapies.

It outlines the regulatory pathway, goals of nonclinical programs, and opportunities for data leveraging. Then, it separately outlines study and safety assessment recommendations for the FIH trial for Gene Editing products and ASOs, followed by guidance on studies to support approval for each type of therapy.

Under the Clinical section, the Guidance emphasizes safety, planning, and data quality, requiring substantial evidence of effectiveness. “Given the very small number of patients expected to be treated, early planning is critical to identify the potential sources of efficacy and safety data for the product to support a future marketing application. FDA anticipates that the first-in-human clinical investigation that will open an IND will also be the primary source of evidence to support approval; therefore, protocols should be designed to be adequate and well-controlled.”

Timely and urgently needed: potential benefits of the Plausible Mechanism Pathway

The Plausible Mechanism Pathway is mainly for cases like Baby KJ’s, where quick, targeted therapies can be lifesaving. For patients with rare diseases, this path could potentially mean no longer having to wait years for treatment, but only months.

Currently, single patients can receive treatment from investigational therapies in clinical trials under the expanded access, without an expectation that the data be used. In contrast, therapies developed under the plausible mechanism pathway could be used to generate critical clinical safety and efficacy data to be used in developing products that can be modified to address other genetic mutations (1).

Additionally, according to the NEJM article “sponsor will be tasked, as a postmarketing commitment, with collecting real-world evidence to confirm continued preservation of efficacy and to show that there were no off-target edits… as well as to study the effect of early treatment on childhood growth and developmental milestones and to detect unexpected safety signals” (1).

The FDA Guidance clarifies that, “FDA may require that data on safety continue to be collected in the post-marketing setting. This may also include collection of efficacy outcomes if there is evidence of a potential for loss of efficacy over time… FDA also intends to closely monitor reports of adverse events from the trial and any signals of unexpected or delayed adverse events in the post-market setting. If a safety signal emerges, FDA will investigate the signal to determine if any action is warranted.” Further recommendations are also found in existing FDA Guidance documents mentioned previously.

While rare diseases, especially those that are fatal or linked to severe childhood disability, will be prioritized under this pathway, Makary and Prasad say a Plausible Mechanism Pathway will also be available for common diseases, specifically conditions that lack proven alternative treatments or have a large unmet need after trying available therapy (1). “For instance, a single disease with 150 different genetic mutations with the same functional implication may require 150 different therapies, and the Plausible Mechanism Pathway would be ideally suited to such therapies,” they state (1).

In this, the two documents differ. The FDA Guidance narrows the scope to only encompass individualized therapies, going on to definine them as “For the purposes of this guidance, individualized therapies are considered therapies that target a specific pathophysiologic abnormality serving as the root cause of a disease, for example, specific pathogenic genetic variant(s) causing a severely debilitating or life-threatening disease or condition in a small number of patients where a randomized controlled trial typically is not feasible.”

An editorial response to the NEJM article that was published in Molecular Therapy characterizes the pathway as important, timely, and urgently needed (2). Timothy Yu, one of the lead authors of the article, writes that reserving the pathway for interventions grounded in compelling genetic evidence of a correctable mechanism will ensure its integrity. For example, it could apply to “strategies that directly address the primary molecular defect in well-characterized monogenic disorders, such as restoring functional gene expression in a loss-of-function condition, specifically knocking down the expression of a nonessential but toxic gene product, or precisely correcting disease-causing mutations back to wild-type sequences” (2).

Additionally, Yu proposes that sponsors using this pathway should be required to submit data about the manufacturing processes and outcomes to a centralized evidence base, allowing the industry to learn from each treated patient. “Analysis of pooled preclinical, clinical, and post-marketing data will be required to assess overall outcomes, refine regulatory requirements and best practices, assess safety signals, and accelerate collective learning for this new pathway in a responsible manner” (2). Products approved under this framework would have met the same safety and efficacy standards as other FDA-approved therapeutics (2).

The FDA Guidance also emphasizes this, with an entire section on the importance of data sharing, which states, “Shared learning through appropriate data sharing is one opportunity to facilitate continued research.”

“A final imperative is timely development of consistent reimbursement models by payors to ensure equitable patient access and continued investment,” Yu notes. “Fatal or very serious disorders of children are prime candidates for these therapies, and time is of the essence if intervention is to be successful.”

Yu views this new pathway not just as a niche fix, but as a way to advance individualized genetic medicines into routine clinical practice for patients and families affected by these rare conditions worldwide (2).

Unclear criteria and risk of becoming the norm: potential risks and criticisms of the NEJM Article

Enthusiasm for the new pathway is high, and some concerns are not about the plausible mechanism idea but about the approach and how it could be extended beyond narrowly defined cases. While there’s consensus that a new pathway is needed for individualized therapies, some regulatory experts and bioethicists caution that the pathway could be used to push forward treatments with less certain efficacy or those with enough patients for which a rigorous, controlled trial should take place, for the benefit of patients.

Holly Fernandez Lynch, a bioethicist at the University of Pennsylvania and the lead author of an editorial published in Health Affairs Forefront, which responded to Makary and Prasad’s article, explains that the concern is not about the plausible mechanism idea. Instead, one of the bigger concerns is that the fuzzy legal process initially used to announce the pathway may leave it open to legal disagreements with companies that believe they should be eligible for the Plausible Mechanism Pathway.

Additionally, Lynch says, “the concern is that they’ve done it out of compliance with the good guidance practice regulations, which specifically say that if you’re making a substantial change to FDA policy, you cannot announce that to the public for the first time through media interviews and through journal articles, which is exactly what they did here.” Instead, Lynch says a guidance document that would have provided more detail on the pathway’s legal authority should have been created first. Lynch explains that this type of document would’ve informed the regulated community of precise details and given people an opportunity to weigh in.

Lynch also says the criteria of the Plausible Mechanism Pathway are unclear, explaining that Makary and Prasad list out the five characteristics of Baby KJ’s case but do not specify if all five need to be present to meet the requirements.

And then there are the scope concerns, and the risk of approving therapies that seem promising in theory but fail in practice. She explains that the drug Sarepta — approved for treating Duchenne muscular dystrophy — is one such example. Despite Sarepta having four drugs approved for the disease, all with a plausible mechanism, none have shown any clinical benefit in clinical trials, and one recent trial testing two of the drugs demonstrated little difference between placebo and treatment.

“We know that when the FDA opens the door to these things, there’s a lot of pressure … to then open the door a little wider and then a little wider and then a little wider until you have an exceptional program becoming the norm,” says Lynch. “These are desperate disease areas, and so sponsors and patient groups are going to be grasping at anything that could be beneficial to them here.”

This has happened before: in 1992, the FDA dismissed concerns that a new accelerated approval pathway designed for getting drugs to dying AIDS patients more quickly would become the norm for drug approval. Now, nearly a third of oncology drugs are approved this way, many of which have not demonstrated an improved survival rate.

Additionally, Makary and Prasad write about expanding the pathway beyond cases like Baby KJ, and Lynch questions what the limits would then be. She argues that it should apply only when a traditional randomized trial is not feasible, keeping it as close as possible to an n-of-1 or n-of-a-few design. “The concern is: How strictly are those characteristics or requirements going to be interpreted once FDA rolls this out? How strict are they going to be about confirming that the target was successfully drugged, or improvement in clinical outcomes?”

Yet others see it as being clearly “designed to evaluate personalized, N=1 therapies—treatments so individualized that traditional randomized controlled trials are impossible.” This editorial goes on to state that “the PMP is intentionally narrow and relies on biological clarity… is not intended for common or biologically complex diseases.”

The FDA Guidance document addresses many of these concerns, and the FDA is accepting comments on the Draft Guidance through April 27, 2026, allowing stakeholders to provide the necessary input.

Future of the Plausible Mechanism Pathway

The fast approval of Baby KJ’s therapy likely saved the infant’s life. While researchers are still in the early stages of understanding the extent to which his bespoke therapy has benefited him, he will likely live with a milder form of his disease. The Plausible Mechanism Pathway aims to drastically shorten development timelines for future individualized medicines, providing hope for patient populations that typically have no treatment options.

However, Prasad and Makary caution that disciplined implementation will be imperative to the pathway’s success. By prioritizing mechanisms over outcomes, there is a risk of approving therapies that seem promising in theory but fail in practice. Additionally, without data from randomized control trials, it’s harder to assess the true benefits versus placebo effects or natural disease progression. As Lynch noted, there is potential for companies to pressure the FDA to accept drugs that don’t necessarily fit the pathway’s mould, and for that to become the norm.

This tension over evidentiary standards and regulatory flexibility has come into sharper focus amid recent leadership changes at the agency: on March 6, it was announced that Prasad would be stepping down as director of the FDA’s Center for Biologics Evaluation and Research. Prasad’s departure follows criticism from the biotech and pharmaceutical industries, which have accused the FDA of reversing previous guidance on the evidence they can use to support their applications. In the past year, the agency has rejected or deferred approval for at least eight drugs for rare diseases, citing issues with the data companies provided to support their applications. However, this has raised questions about how consistently the FDA applies the regulatory flexibility it promotes.

As for the plausible mechanism pathway, the Prasad and Makary article states that the FDA is always open to additional feedback and suggestions regarding it. “Meanwhile,” they state, “for patients and families, there is no time to wait.”

The swift release of the FDA Draft Guidance and commentary in its press release supports this view. “We anticipate our Plausible Mechanism draft guidance will inspire industry to place increased focus on individualized therapies, thereby driving innovation, improving safety, lowering costs and offering more patients with ultra-rare diseases a unique shot at a life-saving treatment.”

References:

1. Prasad V, Makary MA. FDA’s New Plausible Mechanism Pathway. N Engl J Med. 2025 Dec 11;393(23):2365-2367. doi: 10.1056/NEJMsb2512695. Epub 2025 Nov 12. PMID: 41223362.
2. Yu TW, Vitarello J, Musunuru K, Ahrens-Nicklas RC, Liu DR, Mellion ML, Urnov F, Yan W, Chunduru S, Barrett D, Flotte TR, Woodcock J. Response to the FDA’s proposed pathway for individualized genetic therapies. Mol Ther. 2026 Jan 7;34(1):1-2. doi: 10.1016/j.ymthe.2025.12.032. Epub 2025 Dec 29. PMID: 41468889.
3. FDA Draft Guidance: Considerations for the use of the Plausible Mechanism Framework to Develop Individualized Therapies that Target Specific Genetic Conditions with Known Biological Cause. 2026 Feb 25.

Disclaimer:

“The views, opinions, findings, and conclusions or recommendations expressed in these articles and highlights are strictly those of the author(s) and do not necessarily reflect the views of the Oligonucleotide Therapeutics Society (OTS). OTS takes no responsibility for any errors or omissions in, or for the correctness of, the information contained in these articles. The content of these articles is for the sole purpose of being informative and is not intended as an endorsement of any company, technology, or therapeutic that is mentioned. The content is not and should not be used or relied upon as medical, legal, financial, or other advice. Nothing contained on OTS websites or published articles/highlights is intended by OTS or its employees, affiliates, or information providers to be instructional for medical diagnosis or treatment. It should not be used in place of a visit, call, consultation, or the advice of your physician or other qualified health care provider. Always seek the advice of your physician or qualified health care provider promptly if you have any healthcare-related questions. You should never disregard medical advice or delay in seeking it because of something you have read on OTS or an affiliated site.”

Date: October 1, 2026
Time: 11-12pm EDT / 5-6pm CEST

Title: Immunogenicity Risk Assessment for Nucleic Acid Therapeutics: A Comprehensive Evaluation for ASO, siRNA, and Nonvaccine mRNA/LNP Therapies

Description:

Nucleic acid therapeutics require new immunogenicity evaluation frameworks, as the safety and efficacy of these therapies can be impacted by immune responses triggered by different molecular components of these drugs (ASO, siRNA, and non-vaccine mRNA/LNP). This webinar will cover recommendations on conducting immunogenicity risk assessments and developing the right monitoring strategies to get these therapies safely to patients.

Speaker:

Date: September 17, 2026
Time: 11-12pm EDT / 5-6pm CEST

Title: Streamlining Exon-Skipping Antisense Oligonucleotide Therapy Development Via a High-Throughput Approach

Description:

Disease-modifying therapies are available for <5% of the >7000 described rare genetic diseases (RGDs). Antisense oligonucleotides (ASOs) represent a promising precision therapy platform for novel RGD therapies, with a leading approach being ASO-mediated ‘skipping’ of an exon containing a deleterious variant to rescue protein function. However, major challenges in this field are that comprehensive analyses identifying exons amenable to ASO-mediated skipping are non-existent, and patient identification and ASO design remain reactive and slow processes. We therefore sought to proactively identify skippable exons across the genome and design ASO sequences that target these exons, shared as an open-access resource.

Speaker:

Hailey was born a healthy baby, her mom says, hitting all her infant milestones like rolling over and sitting up. But at nine months old, she began falling over when she sat up and having constipation and little sleep. Her concerned mom brought it up at a pediatric appointment, but she was dismissed as being a nervous first-time parent. Four months later, the little girl had her first grand mal seizure. These seizures, along with a failure to thrive and her other initial symptoms, continued. At 16 months, she took her first steps but was always falling and was behind on her speech and other milestones. At 23 months, Hailey had a 90-minute seizure and was airlifted to a children’s hospital. After an MRI and blood tests, the doctors declared her fine. It wouldn’t be until Hailey was six that she finally received a diagnosis of Alexander disease, a rare neurological condition.

Previously, no drugs existed that could change the course of the disease, and treatments focused on managing symptoms. However, Ionis Pharmaceuticals’ therapy, called zilganersen, recently received a breakthrough therapy designation from the Food and Drug Administration (FDA), based on encouraging clinical trial results of patients with Alexander disease.

Alexander Disease: rare, progressive, and fatal

Alexander disease is an ultra-rare, progressive neurological disorder that causes severe disability and death. The disorder is estimated to occur in around one in one to three million people worldwide. Symptoms can first appear in newborns or at any time throughout childhood and into young adulthood, with most children displaying symptoms by age four. An earlier onset typically means a more severe disease and a less likely outcome of surviving past adolescence. If the onset occurs after the age of four, symptoms may be less severe and progress more slowly. While it’s rare, older adults can also be diagnosed with Alexander disease, usually with milder symptoms.

Seizures, muscle stiffness (especially an inability to control muscles for swallowing, airway protection, and purposeful movements), and developmental delays are hallmark symptoms of the disease, which can also cause an enlarged brain and/or head, hydrocephalus, feeding problems, and sleep disorders, depending on the age of onset. The disease usually leads to death within 14-25 years after symptom onset. Classified as a leukodystrophy, a group of genetic conditions that affects the brain’s white matter, Alexander disease can be further categorized as a neurodegenerative leukodystrophy, meaning that over time, neurons lose their structure and functionality.

The disease is typically caused by mutations in the GFAP gene on chromosome 17, leading to an overproduction of an abnormal form of glial fibrillary acidic protein (GFAP). The excess GFAP then causes protein clumps to form in the arms of astrocytes, which are specialized glial cells in the central nervous system. These protein clumps, known as Rosenthal Fibers, may accumulate in the cerebral cortex, white matter of the brain, brainstem, and spinal cord, ultimately causing progressive damage to the nervous system and the symptoms of Alexander disease.

In Hailey’s case, when she was five, she had learning disabilities, speech delays, was unable to walk far, and had an abnormally big head. Around this time, doctors tested her for leukodystrophy, but the results were negative. However, a young doctor became Hailey’s neurologist and was determined to find a diagnosis. She was signed up for a study on children with epilepsy, which included a brain MRI, and she was also tested for Alexander disease.

A combination of clinical presentation, brain magnetic resonance imaging (MRI) findings, and genetic testing is used to diagnose the disease. Interventions, including physiotherapy, speech therapy, nutrition, and anti-epileptic drugs, can help manage symptoms as the disease progresses. But before zilganersen — an antisense oligonucleotide therapy that blocks the excess production of GFAP caused by a mutation in the GFAP gene  — no treatments existed that actually aimed to stop the accumulation of the damaging protein.

The global trial and results: statistically significant and clinically meaningful

The breakthrough therapy designation was granted based on results from a phase 1-3 multiple ascending dose study that assessed the safety and efficacy of zilganersen in 54 participants aged 1.5 to 53 years with genetically confirmed Alexander disease. The participants, most of whom were children, were randomly assigned 2:1 to receive either 25mg or 50mg of zilganersen or placebo via intrathecal bolus (ITB) once every 12 weeks for a 60-week double-blind treatment period. After the 60-week double-blind period, participants transitioned into open-label treatment, followed by a 120-week long-term extension phase, in which those receiving the 25 mg dose began receiving 50 mg.

Results of the global trial, which took place across 13 sites in eight countries, showed that those receiving the 50mg dose of zilganersen had a statistically significant and clinically meaningful improvement from baseline in gait speed compared to placebo at week 61, as assessed by the 10-meter walk test, which found a mean improvement of 33% in patients given the higher dose. The results also demonstrated consistent favorable trends across key secondary endpoints, including patient- and clinician-reported measures that indicate slowed disease progression, stabilization, or improvement. The therapy was safe and well-tolerated, with most adverse events being mild or moderate. Serious adverse events occurred less often in the zilganersen group than in the placebo group.

“People living with Alexander disease have gone far too long without a treatment capable of changing the course of their disease, which makes this Breakthrough Therapy designation particularly meaningful,” said Holly Kordasiewicz, PhD, Executive Vice President, Chief Development Officer at Ionis, in a press statement. “Our pivotal zilganersen study provides the first evidence that an investigational treatment can modify the underlying disease and improve outcomes, representing an important step forward for the Alexander disease community.”

An open-label sub-study for patients under age two continues, and enrolled participants can access zilganersen in the long-term extension.

Previous trial and FDA designations

In 2020, zilganersen was granted Orphan Drug designation and Rare Pediatric designation by the U.S. Food and Drug Administration (FDA). Additionally, in 2019, the European Medicines Agency (EMA) granted zilganersen an Orphan Drug designation.

In 2021, Ionis Pharmaceuticals successfully treated rats exhibiting features of Alexander disease with zilganersen. The study found that rats treated at three weeks old, before the onset of noticeable symptoms, were physically indistinguishable from normal rats. The group that was treated at eight weeks old, when severe impairment was present, had the Rosenthal fibres disappear within a few weeks after one injection, and several disease markers returned to levels close to normal (1).  The encouraging results of this study enabled Ionis to continue on to the recent clinical trial.

Future of zilganersen and those with Alexander disease

After Hailey received the diagnosis, she continued to attend school with the help of an aide. Recently, the now 20-year-old graduated from high school.

“Hailey loves to draw in her sketchbook, enjoys watching cooking shows, and wants to be a chef when she grows up,” her mom says. “She has quite a collection of Barbie dolls, loves the color pink, shopping, and trying new restaurants.”

Despite this, the young woman still has significant learning disabilities, struggles to walk, and has a speech that is difficult to understand, her mom says.

“A treatment could mean Hailey could stay stable, or perhaps it might get her walking better and not need her wheelchair,” her mom says. “I believe it will happen and increase her quality of life.”

The breakthrough therapy designation is a positive step forward for patients like Hailey and their families, with zilganersen providing a potential treatment for not just managing symptoms, but changing the course of their disease. According to the company, Ionis plans to file a new drug application in the early months of 2026 and is working to initiate an expanded patient access program in the U.S.

References:

1. 1. Hagemann TL, Powers B, Lin NH, Mohamed AF, Dague KL, Hannah SC, Bachmann G, Mazur C, Rigo F, Olsen AL, Feany MB, Perng MD, Berman RF, Messing A. Antisense therapy in a rat model of Alexander disease reverses GFAP pathology, white matter deficits, and motor impairment. Sci Transl Med. 2021 Nov 17;13(620):eabg4711. doi: 10.1126/scitranslmed.abg4711. Epub 2021 Nov 17. PMID: 34788075; PMCID: PMC8730534.

“The views, opinions, findings, and conclusions or recommendations expressed in these articles and highlights are strictly those of the author(s) and do not necessarily reflect the views of the Oligonucleotide Therapeutics Society (OTS). OTS takes no responsibility for any errors or omissions in, or for the correctness of, the information contained in these articles. The content of these articles is for the sole purpose of being informative. The content is not and should not be used or relied upon as medical, legal, financial, or other advice. Nothing contained on OTS websites or published articles/highlights is intended by OTS or its employees, affiliates, or information providers to be instructional for medical diagnosis or treatment. It should not be used in place of a visit, call, consultation, or the advice of your physician or other qualified health care provider. Always seek the advice of your physician or qualified health care provider promptly if you have any healthcare-related questions. You should never disregard medical advice or delay in seeking it because of something you have read on OTS or an affiliated site.”