Some Recent Challenging News from Gene Therapy Companies: Sarepta’s Gene Therapy Halted by FDA, Spark Therapeutics Program Gets a Realignment and Review from Roche
Curator: Stephen J.Williams, Ph.D.
Sarepta Therapeutics has received a order from the FDA to halt clinical trials on its Duchenne Muscular Dystrophy gene therapy Elevidys on July 18, 2025 following three deaths.
From FDA: https://www.fda.gov/news-events/press-announcements/fda-requests-sarepta-therapeutics-suspend-distribution-elevidys-and-places-clinical-trials-hold
FDA Requests Sarepta Therapeutics Suspend Distribution of Elevidys and Places Clinical Trials on Hold for Multiple Gene Therapy Products Following 3 Deaths
For Immediate Release:
July 18, 2025
The U.S. Food and Drug Administration today announced it has placed Sarepta Therapeutics investigational gene therapy clinical trials for limb girdle muscular dystrophy on clinical hold following three deaths potentially related to these products and new safety concerns that the study participants are or would be exposed to an unreasonable and significant risk of illness or injury. The FDA has also revoked Sarepta’s platform technology designation.
The FDA leadership also met with Sarepta Therapeutics and requested it voluntarily stop all shipments of Elevidys today. The company refused to do so.
“Today, we’ve shown that this FDA takes swift action when patient safety is at risk.” said FDA Commissioner Marty Makary, M.D., M.P.H. “We believe in access to drugs for unmet medical needs but are not afraid to take immediate action when a serious safety signal emerges.”
The three deaths appear to have been a result of acute liver failure in individuals treated with Elevidys or investigational gene therapy using the same AAVrh74 serotype that is used in Elevidys. One of the fatalities occurred during a clinical trial conducted under an investigational new drug application for the treatment of Limb Girdle Muscular Dystrophy.
“Protecting patient safety is our highest priority, and the FDA will not allow products whose harms are greater than benefits. The FDA will halt any clinical trial of an investigational product if clinical trial participants would be exposed to an unreasonable and significant risk of illness or injury,” said Director of the FDA’s Center for Biologics Evaluation and Research Vinay Prasad, M.D., M.P.H.
Elevidys is an adeno-associated virus vector-based gene therapy using Sarepta Therapeutics, Inc.’s AAVrh74 Platform Technology for the treatment of Duchenne muscular dystrophy (DMD). It is designed to deliver into the body a gene that leads to production of Elevidys micro-dystrophin, a shortened protein (138 kDa, compared to the 427 kDa dystrophin protein of normal muscle cells) that contains selected domains of the dystrophin protein present in normal muscle cells. The product is administered as a single intravenous dose.
Duchenne muscular dystrophy is a rare and serious genetic condition which worsens over time, leading to weakness and wasting away of the body’s muscles. The disease occurs due to a defective gene that results in abnormalities in, or absence of, dystrophin, a protein that helps keep the body’s muscle cells intact.
Further, today, the FDA revoked the platform technology designation for Sarepta’s AAVrh74 Platform Technology because, among other things, given the new safety information, the preliminary evidence is insufficient to demonstrate that AAVrh74 Platform Technology has the potential to be incorporated in, or utilized by, more than one drug without an adverse effect on safety.
Elevidys received traditional approval for use in ambulatory DMD patients 4 years of age and older with a confirmed mutation in the DMD gene on June 20, 2024. It was approved for non-ambulatory patients on June 22, 2023 under the accelerated approval pathway. This pathway can allow earlier approval based on an effect on a surrogate endpoint or intermediate clinical endpoint that is reasonably likely to predict clinical benefit, while the company conducts confirmatory studies to verify the predicted clinical benefit. Continued approval for non-ambulatory patients is contingent upon verification and description of clinical benefit in a confirmatory trial. Given the new safety information, The FDA has notified the company that the indication should be restricted to use in ambulatory patients. The FDA is committed to further investigating the safety of the product in ambulatory patients and will take additional steps to protect patients as needed.
On July 18 Sarepta appeared to be disregarding the FDA release (according to the New York Times)
Source: https://www.nytimes.com/2025/07/18/health/fda-sarepta-elevidys-duchenne.html
Published July 18, 2025
In a remarkable public dispute between drugmaker and regulator, the biotech company Sarepta Therapeutics is defying the Food and Drug Administration’s request that it halt distribution of its treatment for a deadly muscle-wasting disease.
In a news release on Friday evening, the agency said that it requested that the company voluntarily stop all shipments of the therapy, known as Elevidys, citing the deaths of three patients from liver failure who had taken the product or a similar therapy.
In its own news release later on Friday evening, Sarepta, which is based in Cambridge, Mass., said that it would continue to ship the treatment for patients who do not use wheelchairs. The company said its analysis showed no new safety problems in those patients and that it was committed to patient safety.
Dr. Marty Makary, the F.D.A. commissioner, said in the agency’s statement that its request to Sarepta demonstrated that the F.D.A. “takes swift action when patient safety is at risk.”
“We believe in access to drugs for unmet medical needs but are not afraid to take immediate action when a serious safety signal emerges,” he said.
In the past, the F.D.A. has sometimes asked companies to pause distribution of a drug until a new problem is better understood and mitigated. However, it can also press its case, and begin a process to revoke the drug’s license, which would begin with a formal notification and opportunity to respond and participate in a public hearing.
On July 21, 2025 Sarepta announces on their website in press release
Sarepta Therapeutics Announces Voluntary Pause of ELEVIDYS Shipments in the U.S.
07/21/25 7:40 PM EDT
CAMBRIDGE, Mass.–(BUSINESS WIRE)–Jul. 21, 2025– Sarepta Therapeutics, Inc. (NASDAQ:SRPT), the leader in precision genetic medicine for rare diseases, today issued the following statement:
Today, Sarepta Therapeutics notified the U.S. Food and Drug Administration (FDA) of its decision to voluntarily and temporarily pause all shipments of ELEVIDYS (delandistrogene moxeparvovec) for Duchenne muscular dystrophy in the United States, effective close of business Tuesday, July 22, 2025.
This proactive step will allow Sarepta the necessary time to respond to any requests for information and allow Sarepta and FDA to complete the ELEVIDYS safety labeling supplement process. The Company looks forward to a collaborative, science-driven review process and dialogue with the FDA.
“As a patient-centric organization, the decision to voluntarily and temporarily pause shipments of ELEVIDYS was a painful one, as individuals with Duchenne are losing muscle daily and in need of disease-modifying options,” said Doug Ingram, chief executive officer, Sarepta. “It is important for the patients we serve that Sarepta maintains a productive and positive working relationship with FDA, and it became obvious that maintaining that productive working relationship required this temporary suspension while we address any questions that FDA may have and complete the ELEVIDYS label supplement process.”
Sarepta remains committed to transparency and patient safety and will continue to provide timely updates to patients, families, healthcare providers, and the broader Duchenne community as additional information becomes available.
About ELEVIDYS (delandistrogene moxeparvovec-rokl)
ELEVIDYS (delandistrogene moxeparvovec-rokl) is a single-dose, adeno-associated virus (AAV)-based gene transfer therapy for intravenous infusion designed to address the underlying genetic cause of Duchenne muscular dystrophy – mutations or changes in the DMD gene that result in the lack of dystrophin protein – through the delivery of a transgene that codes for the targeted production of ELEVIDYS micro-dystrophin in skeletal muscle.
ELEVIDYS is indicated for the treatment of Duchenne muscular dystrophy (DMD) in individuals at least 4 years of age.
- For patients who are ambulatory and have a confirmed mutation in the DMD gene
- For patients who are non-ambulatory and have a confirmed mutation in the DMD gene.
However this is not the first time Sarepta has been in the hot seat…
Read this interesting article from Derrick Lowe of Science. I will put it in its entirety as Derick Lowe really writes some great articles in his blog.
Source: https://www.science.org/content/blog-post/sarepta-why
Sarepta. Why? 21 Jun 2024
I really, really wish that I were not writing about Sarepta again. But here we are. Perhaps a quick review will explain my reluctance.
Back in 2013, the company was trying to get approval for an unusual “exon skipping” molecule (eteplirsen) as a therapy for Duchenne muscular dystropy. Nothing wrong with that – in fact, there’s a lot that’s right with that, since Duchenne is a perfect “unmet medical need” situation, and the exon-skipping idea was an innovative approach ten years ago (and it’s still not exactly a standard-issue therapy). Attacking very hard-to-treat diseases with new mechanisms of action is just what we’re supposed to be doing in this business.
The approval, though, was having trouble for some very good reasons. Sarepta’s trial was very, very small and the FDA later found that their trial design was very, very flawed. But in 2016 eteplirsen was suddenly approved, to the surprise of many observers (including me). A few years later, a follow-up drug (golodirsen) from the company (golodirsen) was also rejected by the FDA (with a Complete Response Letter) but then was later suddenly approved, although no new data had been presented. That was particularly mystifying since the eventually-published CRL detailed a number of real problems with eteplirsen since its approval, problems that looked to be possibly even greater with the follow-up drug. To the best of my knowledge, the confirmatory Phase III trial that was required at the time of golodirsen’s approval is still going on and is expected to read out next year. In 2021, another Sarepta exon-skipping drug (different exon this time) was approved (casimirsen) on the basis of biomarker levels that were expected to show eventual clinical benefit, and I believe that its confirmatory trial is part of the golodirsen one. That one at least did not go through the first-rejected-then-approved pathway.
More recently the company has been working on an outright gene therapy (elevidys) for Duchenne, and the initial results were quite promising. The company got accelerated FDA approval for that one last June for 4- and 5-year-old patients, even though actual clinical benefit had not yet been established. But gene therapy is a winding road, and last October the Phase III results for Elevidys were a complete miss in the primary endpoint. Arguing commenced, with the company saying that the results in the secondary endpoints showed that the drug was “modifying the trajectory” of the disease, and the CEO called the results a “massive win” and said that the company would use them to ask for a much wider label approval from the FDA. Apparently during the conference call, when he was asked about why he was so confident, he said that the FDA’s CBER head Peter Marks was “very supportive”. (It should be noted that since then another Duchenne gene therapy effort, this one from Pfizer, also failed its Phase III, so it’s not like this is a straightforward area).
Boy, was that the truth. The agency has just granted that use expansion, and it turns out that it was all due to Peter Marks, who completely overruled three review teams and two of his highest-level staffers (all of whom said that Sarepta had not proven its case). Honestly, I’m starting to wonder why any of us go to all this trouble. It appears that all you need is a friend high up in the agency and your clinical failures just aren’t an issue any more. Review committees aren’t convinced? Statisticians don’t buy your arguments? Who cares! Peter Marks is here to deliver hot, steaming takeout containers full of Hope.
Back in 2016, when eteplirsen first came up for its advisory committee vote, I wrote that there was a matrix of possible votes and interpretations, which I summed up this way:
(1) A negative vote, which is a rejection of the potential of the drug, the suffering of DMD patients, and their right to try a therapy which apparently does no harm, for a disease that has no other options.
(2) A negative vote, which is the only possible one, considering that the company’s trial data are far too sparse and unconvincing to allow a recommendation to approve the drug. If this gets recommended, what doesn’t? Why do we require new drugs to show efficacy at all?
(3) A positive vote, which is a victory for patient advocates everywhere, and in particular for the extremely ill boys who suffer from this disease, or. . .
(4) A positive vote, which marks an undeserved and potentially hazardous victory of emotional rhetoric and relentless patient advocacy over the scientific and medical evidence.
As I’ve said many times since, including just a few days ago, I believe that the FDA is tilting very, very noticeably towards #4 while proclaiming the wonderful new world of #3. And while I realize that this may make me sound like a heartless SOB, I think this is a huge mistake that we will be paying for for a long time.
Note that there has been reported deaths in 2024.
The following was from some data published in Nature in 2025 from Clinical Trial ClinicalTrials.gov: NCT05096221.
Mendell JR, Muntoni F, McDonald CM, Mercuri EM, Ciafaloni E, Komaki H, Leon-Astudillo C, Nascimento A, Proud C, Schara-Schmidt U, Veerapandiyan A, Zaidman CM, Guridi M, Murphy AP, Reid C, Wandel C, Asher DR, Darton E, Mason S, Potter RA, Singh T, Zhang W, Fontoura P, Elkins JS, Rodino-Klapac LR. AAV gene therapy for Duchenne muscular dystrophy: the EMBARK phase 3 randomized trial. Nat Med. 2025 Jan;31(1):332-341. doi: 10.1038/s41591-024-03304-z
Abstract
Duchenne muscular dystrophy (DMD) is a rare, X-linked neuromuscular disease caused by pathogenic variants in the DMD gene that result in the absence of functional dystrophin, beginning at birth and leading to progressive impaired motor function, loss of ambulation and life-threatening cardiorespiratory complications. Delandistrogene moxeparvovec, an adeno-associated rh74-viral vector-based gene therapy, addresses absent functional dystrophin in DMD. Here the phase 3 EMBARK study aimed to assess the efficacy and safety of delandistrogene moxeparvovec in patients with DMD. Ambulatory males with DMD, ≥4 years to <8 years of age, were randomized and stratified by age group and North Star Ambulatory Assessment (NSAA) score to single-administration intravenous delandistrogene moxeparvovec (1.33 × 1014 vector genomes per kilogram; n = 63) or placebo (n = 62). At week 52, the primary endpoint, change from baseline in NSAA score, was not met (least squares mean 2.57 (delandistrogene moxeparvovec) versus 1.92 (placebo) points; between-group difference, 0.65; 95% confidence interval (CI), -0.45, 1.74; P = 0.2441). Secondary efficacy endpoints included mean micro-dystrophin expression at week 12: 34.29% (treated) versus 0.00% (placebo). Other secondary efficacy endpoints at week 52 (between-group differences (95% CI)) included: Time to Rise (-0.64 (-1.06, -0.23)), 10-meter Walk/Run (-0.42 (-0.71, -0.13)), stride velocity 95th centile (0.10 (0.00, 0.19)), 100-meter Walk/Run (-3.29 (-8.28, 1.70)), time to ascend 4 steps (-0.36 (-0.71, -0.01)), PROMIS Mobility and Upper Extremity (0.05 (-0.08, 0.19); -0.04 (-0.24, 0.17)) and number of NSAA skills gained/improved (0.19 (-0.67, 1.06)). In total, 674 adverse events were recorded with delandistrogene moxeparvovec and 514 with placebo. There were no deaths, discontinuations or clinically significant complement-mediated adverse events; 7 patients (11.1%) experienced 10 treatment-related serious adverse events. Delandistrogene moxeparvovec did not lead to a significant improvement in NSAA score at week 52. Some of the secondary endpoints numerically favored treatment, although no statistical significance can be claimed. Safety was manageable and consistent with previous delandistrogene moxeparvovec trials.
As noted in the adobe abstract everything seemed to fine as reported in this trial.
However there was a report of an immunoloically related death in 2023:
For the first time, in June 2023, delandistrogene moxeparvovec (SRP-9001), a gene replacement therapy based on an adeno-associated virus (AAV) vector, was approved in the USA for children aged 4-5 years with DMD. Other promising gene therapies are in preclinical development or clinical trials, including CRISPR/Cas9-mediated strategies to restore dystrophin expression. Two deaths following DMD gene therapy with high-dose AAV vectors were attributed to AAV-mediated immune responses. The pre-existing disease underlying the therapy is most likely involved in the fatal AAV toxicity.
Now this may have been dose related as the patient was given a high dose.
DMD gene therapy death exposes risks of treating older patients
By Nick Paul Taylor May 19, 2023 9:35am
Duchenne muscular dystrophy (DMD) Cell & Gene Therapy gene therapy viral vectors
Cure Rare Disease plans to continue its programs with alternative vectors. (iStock / Getty Images Plus)
Cure Rare Disease has shared a deep dive into the death of the only participant in a gene therapy trial. The nonprofit and its collaborators tied the death of a patient with Duchenne muscular dystrophy (DMD) to an immune reaction to the viral vector, raising concerns about dosing older, more advanced people.
Commercial development of DMD gene therapies has focused on younger patients, with Sarepta Therapeutics limiting enrollment in its phase 3 trial to children aged 4 to 8 years old. The restrictive recruitment criteria have stopped many DMD patients from accessing gene therapies in clinical trials run by Sarepta and its rivals. The patient dosed in the Cure Rare Disease clinical trial was 27 years of age, and the therapy had been designed for him.
Last year, the nonprofit reported that the patient, who was the brother of its CEO, died after receiving the therapy. The death led to an investigation into what happened after the patient received the therapy, which was designed to use CRISPR transactivation to upregulate an alternate form of a key DMD protein.
Writing in preprint journal medRxiv (PDF), Cure Rare Disease described the findings of the investigation. A post-mortem showed injuries to the patient’s lungs, likely caused by a strong immune reaction to the high dose of the adeno-associated virus (AAV) vector that was given to try to ensure sufficient expression to achieve a therapeutic effect. There was minimal expression of the transgene in the liver.
At 1×1014 vg/kg, the studied dose was similar to that tested in other clinical trials but resulted in a higher vector genome load, a finding the researchers attributed to the patient’s lower lean muscle mass, 45%. The analysis suggests the patient had “a more severe innate immune reaction than others receiving similar or slightly higher doses of rAAV in microdystrophin gene therapy trials.”
Based on the finding, the researchers identified a need for more data on the characteristics that may predispose people to severe innate immune reactions and concluded “dose determination will remain a challenge for custom-designed AAV-mediated therapies, as by definition the precise therapeutic dose will not have been established.”
As for the application of CRISPR, the researchers said the toxicity and eventual death of the patient meant that an assessment of the safety and efficacy of the treatment was not possible.
AAV related clinical trials have been halted for drug-induced liver injury, predominantly due to severe immune reaction. In many cases it appears when high dose AAV therapy is used.
Duan D. Lethal immunotoxicity in high-dose systemic AAV therapy. Mol Ther. 2023 Nov 1;31(11):3123-3126. Doi: 10.1016/j.ymthe.2023.10.015
.10.015. Epub 2023 Oct 10. PMID: 37822079; PMCID: PMC10638066.
Abstract
High-dose systemic gene therapy with adeno-associated virus (AAV) is in clinical trials to treat various inherited diseases. Despite remarkable success in spinal muscular atrophy and promising results in other diseases, fatality has been observed due to liver, kidney, heart, or lung failure. Innate and adaptive immune responses to the vector play a critical role in the toxicity. Host factors also contribute to patient death. This mini-review summarizes clinical findings and calls for concerted efforts from all stakeholders to better understand the mechanisms underlying lethality in AAV gene therapy and to develop effective strategies to prevent/treat high-dose systemic AAV-gene-therapy-induced immunotoxicity.
Table 1.
Fatality cases following high-dose systemic AAV delivery
|
Drug name |
AAV |
Clinical profile |
Reference |
| Serotype |
Dose (vg/kg) |
Promoter |
Transgene |
Disease |
Patient age |
Time of death |
Cause of death |
Immunotoxicity |
Clinical trial ID |
| Acute death |
PF-06939926 |
AAV9 |
2 × 1014 |
miniMCK |
μDys gene |
DMD |
16 years |
6 days post-dosing |
heart failure |
innate response |
NCT03362502 |
Lek et al.,8 Philippidis9, and Lek et al.10 |
| CRD-TMH-001 |
AAV9 |
1 × 1014 |
CK8e |
dCas9-VP64 and gRNA |
DMD |
27 years |
8 days post-dosing |
lung failure |
innate response (cytokine-mediated) |
NCT05514249 |
Lek et al.10 |
| Subacute death |
Zolgensma |
AAV9 |
1.1 × 1014 |
CBA |
SMN gene |
SMA |
≤2 years (4 patients) |
5–6 weeks post-dosing |
liver failure |
adaptive response |
post-marketing |
Philippidis, Whiteley, and Kishimoto and Samulski6,19,20 |
| Zolgensma |
AAV9 |
1.1 × 1014 |
CBA |
SMN gene |
SMA |
6 months |
8 weeks post-dosing |
kidney failure |
innate response (complement mediated) |
post-marketing |
Guillou et al.7 |
| AT132 |
AAV8 |
1.3–3 × 1014 |
DES |
MTM1 gene |
XLMTM |
≤5 years (4 patients) |
20–40 weeks post-dosing |
liver fa |
|
|
|
Table from Duan D. Lethal immunotoxicity in high-dose systemic AAV therapy. Mol Ther. 2023 Nov 1;31(11):3123-3126. source: https://pmc.ncbi.nlm.nih.gov/articles/PMC10638066/
Roche Decides to Stop backing Sparks Therapeutics Hemophilia A Gene Therapy Program
In 2019, Roche acquired Children’s Hospital of Pennsylvania (CHOP) spinout Spark Therapeutics for $4.8 billion, one of the largest pharma acquisitions up to that time. It was reported on this site here
https://pharmaceuticalintelligence.com/2019/03/01/spark-therapeutics-4-8billion-deal-confirmed-as-biggest-vc-backed-exit-in-philadelphia/
However as reported by Fierce Biotech (and updated above link) at https://www.fiercepharma.com/pharma/roche-overhauls-spark-gene-therapy-unit-recording-24b-full-impairment Roche will reorganize the company and deal, bringing in Spark into the corporate fold. However this meant massive layoffs and possibly either end of the gene therapy program in order to integrate it with Roche’s current programs. The Spark gene therapy has met with success so it will be interesting to see how Roche continues this program in the future.
However it has been a rough year for many gene therapies.
Other Articles in this Open Access Scientific Journol of Gene Therapy
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This year’s Nobel Prize laureates in chemistry Demis Hassabis and John Jumper have developed an AI model to solve a 50-year-old problem: predicting proteins’ complex structures.
In 2020, Hassabis and Jumper presented an AI model called AlphaFold2. With its help, they have been able to predict the structure of virtually all the 200 million proteins that researchers have identified. Since their breakthrough, AlphaFold2 has been used by more than two million people from 190 countries. Among a myriad of scientific applications, researchers can now better understand antibiotic resistance and create images of enzymes that can decompose plastic.
Read more about their story: https://bit.ly/4diKiJ2