Prime Editing Enters the Clinic: A CRISPR Milestone for Rare Immune Disorders

By Dr. Priyom Bose, Ph.D.Reviewed by Lexie Corner

Clustered, regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (CRISPR-Cas9) are genome editing tools.¹  

After their potential in therapeutics was recognized, scientists focused on improving their clinical performance. This led to the development of prime editing, which enables precise genetic modifications and may help treat rare immune disorders.

Image Credit: Andrii Yalanskyi/Shutterstock.com

How Was Prime Editing Technology Developed?

In 2016, David Liu and his team at Harvard University introduced a new method for precision gene editing called base editing.² Unlike conventional CRISPR techniques, which create double-strand breaks in DNA, base editing changes a single DNA base through deamination. This method uses a modified CRISPR-Cas9 protein fused with a deaminase enzyme to convert specific bases.

Base editing reduces the risk of off-target effects, a known limitation of standard CRISPR-Cas9. However, it allows only four types of base substitutions: cytosine (C) to thymine (T), guanine (G) to adenine (A), T to C, and A to G.

In 2019, Andrew Anzalone, a postdoctoral researcher in Liu's lab, developed prime editing. This approach extends editing capability to all 12 possible base conversions.³ Prime editors (PE) include a modified Cas9 protein linked to reverse transcriptase and a prime editing guide RNA (pegRNA). This system enables targeted DNA changes without causing double-strand breaks.

A pegRNA contains four key parts: the target sequence, scaffold sequence, reverse transcription template, and primer-binding site (PBS).

How Prime Editing Has Evolved in Genetic Research

Prime editing reduces off-target effects by enabling precise base deletions in genetic knockouts and specific nucleotide insertions in knock-ins. Unlike conventional gene editing tools, it allows targeted modifications without the need for a donor DNA template.

Researchers have developed several versions of the prime editor—PE1, PE2, PE3, and PE3b.⁴ These versions offer improved reliability, support for small edits, and greater thermostability, which is important for gene therapy applications. More recently, PE5 introduced further improvements. It incorporates mismatch repair inhibitors (such as MLH1dn) to prevent cellular repair mechanisms from undoing edits, helping ensure the changes remain.

Another advancement is EXPERT (Extended Prime Editor System), a more versatile and precise version of PE.⁵ It uses extended pegRNAs (ext-pegRNAs) and an additional single-guide RNA (ups-sgRNA) to enable edits on both sides of a DNA nick, expanding the range of possible modifications.

Prime editing is already showing promise in both research and therapeutic applications, especially for treating rare genetic disorders and supporting precision medicine.

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Breakthrough Uses of Prime Editing in Therapy

Recent breakthroughs in PE, such as the PM359 clinical trial for chronic granulomatous disease (CGD), have demonstrated the potential of prime editing in treating rare genetic disorders. Below are key milestones in its therapeutic application.

Chronic Granulomatous Disease

CGD is a rare immune disorder affecting approximately 1 in 200,000 to 250,000 people worldwide.⁶ It is marked by increased susceptibility to bacterial and fungal infections due to mutations in one of several genes: CYBA, CYBB, NCF1, NCF2, CYBC1, or NCF4. These genes encode subunits of the NADPH oxidase complex, an enzyme system essential for pathogen clearance by neutrophils.

To address this, scientists developed PM359, a prime editor designed to treat CGD. This strategy targets the p47phox variant of CGD, which is caused by mutations in the NCF1 gene. PM359 addresses limitations of conventional treatments, such as donor hematopoietic stem cell (HSC) transplantation, by reducing the risk of graft-versus-host disease and graft failure.

Preclinical trials have shown that PM359-edited cells can engraft in the bone marrow and restore NADPH oxidase function. In 2024, U.S.-based Prime Medicine received approval from the Food and Drug Administration (FDA) for its Investigational New Drug (IND) application, making PM359 the first PE to enter a clinical trial for CGD treatment.⁷

Sickle Cell Disease

Sickle cell disease (SCD) is a group of inherited blood disorders that affect red blood cells. It is caused by a single-nucleotide mutation in the HBB gene. A proof-of-concept study has shown that prime editing can correct this mutation through precise single-base substitution with high efficiency.⁸

Tay-Sachs Disease

Tay-Sachs disease is a rare and fatal genetic disorder that leads to progressive damage to the nervous system. It results from a lysosomal storage defect caused by a 4-base pair insertion in the HEXA gene. Preclinical studies have demonstrated the potential of prime editing to correct this mutation in HEK293T cells using optimized pegRNAs.⁹

Where Prime Editing Stands Today and What’s Next

Although prime editing shows great promise, its clinical use remains in the early stages. Researchers are actively evaluating its effectiveness across various therapeutically relevant cell types, including stem cells.

Ongoing work focuses on improving the precision of prime editing while maintaining safety. Scientists are also studying the durability and long-term effects of edits, which are key considerations for real-world clinical use.

Findings from preclinical and clinical studies, particularly in rare genetic disorders, suggest that prime editing could become a valuable tool in the development of future treatments.

Learn More About Prime Editing

For a deeper dive into how prime editing works, including the role of pegRNA, nCas9, and reverse transcriptase, watch:

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References and Further Reading

1. Huang YY, et al. Development of clustered regularly interspaced short palindromic repeats/CRISPR-associated technology for potential clinical applications. World J Clin Cases. 2022;10(18):5934-5945. doi: 10.12998/wjcc.v10.i18.5934.
2. Komor AC, et al. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533(7603):420-4. doi: 10.1038/nature17946.
3. Lu C, et al. Prime Editing: An All-Rounder for Genome Editing. Int J Mol Sci. 2022;23(17):9862. doi: 10.3390/ijms23179862.
4. Huang Z, Liu G. Current advancement in the application of prime editing. Front Bioeng Biotechnol. 2023;11:1039315. doi: 10.3389/fbioe.2023.1039315.
5. Xiong, Y, et al. EXPERT expands prime editing efficiency and range of large fragment edits. Nat Commun, 2025; 16, 1592. doi.org/10.1038/s41467-025-56734-9
6. O’Donovan CJ, et al. Diagnosis of Chronic Granulomatous Disease: Strengths and Challenges in the Genomic Era. Journal of Clinical Medicine. 2024; 13(15):4435. doi.org/10.3390/jcm13154435
7. O'Hanlon, K. The FDA Has Cleared the First Clinical Trial Application for a Prime Editor. 2025. Available at: https://crisprmedicinenews.com/news/the-fda-has-cleared-the-first-clinical-trial-application-for-a-prime-editor/
8. Everette, K.A., et al. Ex vivo prime editing of patient haematopoietic stem cells rescues sickle-cell disease phenotypes after engraftment in mice. Nat. Biomed. Eng. 2023;7,616–628. doi.org/10.1038/s41551-023-01026-0
9. Hung JE, et al. Precise template-free correction restores gene function in Tay-Sachs disease while reframing is ineffective. Mol Ther Nucleic Acids. 2024;36(1):102401. doi: 10.1016/j.omtn.2024.102401.