First Personalized CRISPR Therapy for Baby

This report summarizes the key aspects of the personalized CRISPR therapy developed for an infant with CPS1 deficiency.

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The sources describe a historic medical breakthrough where a customized CRISPR gene editing therapy was successfully developed and delivered to an infant named KJ, diagnosed with severe carbamoyl phosphate synthetase 1 (CPS1) deficiency. This personalized therapy was designed and administered by a large team of collaborators led by pediatrician Rebecca Ahrens-Nicklas, M.D., Ph.D., and geneticist Kiran Musunuru, M.D., Ph.D., both affiliated with the Children's Hospital of Philadelphia (CHOP) and the Perelman School of Medicine at the University of Pennsylvania. The results of KJ's treatment were published in The New England Journal of Medicine on May 15 and presented at the American Society of Gene & Cell Therapy (ASGCT) Annual Meeting. Funding for the work came primarily from the National Institutes of Health (NIH).

Carbamoyl Phosphate Synthetase 1 (CPS1) Deficiency

CPS1 deficiency is a rare, inherited genetic disorder affecting the urea cycle. Patients lack a functional carbamoyl phosphate synthetase 1 (CPS1) enzyme, which is crucial for processing ammonia generated during protein digestion in the liver. Without enough of this enzyme, ammonia builds up to toxic levels in the body, threatening serious brain injury and death. This buildup of ammonia, known as hyperammonemia, can occur within 24 to 48 hours after birth. The condition is estimated to kill about half of affected children in early infancy. Over 300 mutations have been identified in the CPS1 gene, including missense and nonsense mutations that lead to reduced or complete loss of protein function.

Typical treatment for CPS1 deficiency includes a low-protein diet, dialysis to remove ammonia, and medications to replace the enzyme's function. The only long-term solution is a liver transplant. However, a liver transplant is extremely risky for critically ill infants like KJ, and there is a high risk of rapid organ failure while waiting for a transplant. High ammonia levels during this waiting period can cause coma, brain swelling, and potentially fatal or permanent brain damage. KJ's condition was initially so severe that his mother stated he wouldn't have survived past day five without immediate intervention.

The Personalized CRISPR Therapy for KJ

The therapy developed for KJ was a personalized gene editing therapy designed to correct the specific mutation in his CPS1 gene. Using a base editing approach, the therapy successfully changed a mutant adenine (A) into an inosine (I) on the non-coding DNA strand, which mimics a guanosine (G), ultimately leading to the production of a full-length CPS1 protein. This base editing strategy is a type of CRISPR-Cas mediated single-base editing that can directly modify mutations without creating double-strand breaks (DSBs) in the DNA, potentially reducing undesired insertions or deletions (indels) compared to conventional Cas9. Specifically, an adenine base editor (ABE) fused to a catalytically deficient Cas9 (dCas9) was used. The designed therapy delivered the adenine base editor and patient-specific guide RNA (gRNA) via lipid nanoparticles to the liver.

The team, including researchers and clinicians at CHOP and Penn, collaborated to study the feasibility of creating customized gene editing therapies for individual patients, building on years of research in rare metabolic disorders and gene editing. They specifically targeted KJ's unique variant of CPS1, identified shortly after his birth. The process, from diagnosis to treatment readiness, took only six months. Preclinical studies, including in vitro and in vivo tests, were conducted to identify the most effective and precise combination of the adenine base editor and guide RNA.

KJ received his first infusion of the experimental therapy in late February 2025, between six and seven months of age. He later received follow-up doses in March and April 2025, receiving three doses in total as of April 2025.

Outcomes and Monitoring

The research team observed positive signs of the therapy's effectiveness almost immediately. In the short time since treatment, KJ has tolerated increased dietary protein and required less nitrogen scavenger medication. Notably, he was able to recover from common childhood illnesses, such as a cold and a gastrointestinal illness, without ammonia building up to dangerous levels, which would normally be extremely risky for a child in his condition. As of the reports, he is growing well and thriving. No serious side effects were reported after the three doses.

The researchers are cautiously optimistic about KJ's progress, but stress that much work remains and that long-term follow-up is crucial to fully evaluate the benefits and monitor for any potential off-target effects, immune responses, or the durability of the therapeutic effect. Additional studies are also needed to examine editing efficiency in liver biopsy samples.

CRISPR Technology and Gene Editing

CRISPR-Cas9 gene editing is based on a natural defense system found in prokaryotes used to identify and degrade foreign genetic material. The gene editing tool consists of two main components: a guide RNA (gRNA) that directs the system to a specific target DNA sequence, and the Cas9 protein, a nuclease that cuts the DNA at the target location. Cas9 recognizes a short DNA sequence called the Protospacer Adjacent Motif (PAM) near the target site to initiate DNA melting and cleavage. The cleaved DNA is then repaired by the cell's natural machinery, which can lead to gene correction or disruption.

Before CRISPR/Cas9, gene editing relied on methods like zinc finger nucleases (ZFNs) and Transcription activator-like effector nucleases (TALENs), but these techniques were challenging, expensive, and time-consuming. CRISPR/Cas9, discovered for its genome editing potential in 2012, became the most effective, efficient, and accurate method for editing genomes in living cells.

Beyond the conventional Cas9 that creates DSBs, newer techniques like single-base editing and prime editing can introduce precise genetic changes with potentially fewer unwanted side effects. Base editors, such as cytidine base editors (CBE) and adenine base editors (ABE), can convert one nucleotide base to another (e.g., C to T or A to G) without creating DSBs. Prime editing, the most recent development, uses a Cas9 nickase fused to a reverse transcriptase and a complex guide RNA to introduce targeted insertions, deletions, and all 12 types of base-to-base changes.

Challenges in Gene Delivery

A significant challenge in gene editing is the safe and effective delivery of the CRISPR/Cas components into target cells. Delivery methods can be categorized as physical, chemical, and viral vectors.

• Physical methods (e.g., electroporation, microinjection) can deliver components but may cause cell damage or are limited in scale.
• Chemical methods (e.g., lipid nanoparticles, polymeric nanoparticles) encapsulate the components and facilitate entry into cells, often via endocytosis. Lipid nanoparticles were used to deliver the therapy to KJ's liver cells.
• Viral vectors, such as adeno-associated viruses (AAVs), are considered natural experts for in vivo delivery due to their efficiency. AAVs are commonly used because of their low immunogenicity and lack of integration into the host genome. However, limitations include packaging capacity for large components and potential immune responses.

Other challenges in developing effective gene delivery systems include limited transfection efficiency, immune responses against the vector or foreign DNA, ensuring target specificity, maintaining the stability of the delivery system, and managing potential toxicity and side effects.

Implications and Future of Personalized Gene Editing

This first successful personalized in vivo gene editing treatment for a rare genetic disease is a major milestone. Researchers hope this approach can be scaled and adapted to treat individuals with other rare diseases for whom no treatments currently exist. The technology platform, built on reusable components and rapid customization, promises a new era of precision medicine that can quickly tailor treatments to individual patients for hundreds of rare diseases.

Kiran Musunuru views this as an early step in a "totally new type of medicine". He envisions a future where gene editing becomes the standard of care for a wide range of diseases, from ultra-rare to the most common, offering potentially durable, long-term therapeutic effects that could relieve patients of the burden of daily chronic therapies. This could transform medicine into a procedural healthcare model with one-time interventions.

For patients with ultra-rare disorders like CPS1 deficiency, these findings offer hope, although validation through treatment of more patients is needed. The success of KJ's treatment could inspire others to use CRISPR for ultra-rare conditions.

Ethical and Regulatory Considerations

The development and use of gene therapy, particularly in pediatric patients, raise significant ethical questions. Open dialogue among diverse stakeholders, including patients, advocates, regulators, industry, clinicians, and ethicists, is considered vital for the ethical development and use of these interventions in children. Discussions highlight the importance of balancing hope and hype, managing uncertainties about new therapies, and ensuring transparency while protecting patient privacy. Risk tolerance varies based on disease severity and alternative treatments; decisions about gene therapy, especially for children, involve complex considerations about future autonomy and potential burdens.

Policy barriers related to newborn screening and genetic testing can delay diagnosis and intervention, impacting patient access to potential treatments. Implementation challenges exist due to state budgets, insurance coverage, reimbursement policies, and the availability of healthcare professionals skilled in translating genomic findings into care. Ethical questions also arise regarding mandatory screening for conditions without available treatments.

Long-term follow-up studies are crucial for identifying delayed or rare adverse events like immune reactions or potential cancer development, informing future clinical decisions. However, these studies must be designed with a patient-centric approach to minimize burdens on families, potentially using telehealth or decentralized testing. Data sharing through collaborative databases is valuable but requires more support and infrastructure.

Ethical considerations also pertain to data sharing, particularly for rare diseases where unique clinical experiences are valuable. While patients are often willing to share data for research, concerns exist about privacy and companies potentially taking advantage of small patient populations for profit, which could hinder data sharing. A more open model for data sharing in the rare disease space is suggested, as traditional competition models are less suitable.

From a regulatory perspective, the role of regulatory affairs in gene therapy has expanded significantly. It now encompasses guiding clinical trial design, ensuring stringent manufacturing standards (CMC), and implementing post-market surveillance for long-term safety. Unique regulatory challenges in gene therapy include safety concerns (immune reactions, off-target effects), long-term efficacy monitoring, and adapting frameworks for personalized treatments. Regulatory professionals must navigate evolving guidelines from bodies like the FDA and EMA, preparing robust data packages for approval. Regulatory bodies are updating guidelines, focusing on post-market surveillance and using adaptive trial designs. CMC processes are critical for the safety, quality, and consistency of gene therapies, requiring comprehensive documentation and oversight of manufacturing. Accelerated approval pathways, like the FDA's Fast Track and Breakthrough Therapy Designation, can expedite review for promising treatments.

Collaboration

A key takeaway from KJ's treatment is the absolute necessity of collaboration. To make this effort a reality, a vast team was required, involving people not just from CHOP and Penn Medicine but also academic colleagues, industry partners who donated expertise and components, and governmental colleagues from around the country and the world, such as the NIH and FDA. Everyone involved dropped what they were doing to help KJ, demonstrating the critical role of interdisciplinary and cross-organizational cooperation, especially for rare disease patients.

References

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From the News-Medical.net source:

• Gropman, A. L., & Komor, A. C. (2025). Personalized Gene Editing to Treat an Inborn Error of Metabolism. New England Journal of Medicine. doi:10.1056/NEJMe2505721, https://www.nejm.org/doi/full/10.1056/NEJMe2505721.

From the CGTLive® source:

• World's first patient treated with personalized CRISPR gene editing therapy at Children’s Hospital of Philadelphia. News release. Children’s Hospital of Philadelphia. May 15, 2025. Accessed May 15, 2025.https://www.chop.edu/news/worlds-first-patient-treated-personalized-crispr-gene-editing-therapy-childrens-hospital.
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From the Nature source:

• Musunuru, K. et al. N. Engl. J. Med. https://doi.org/10.1056/NEJMoa2504747 (2025)..