Is prime editing ready for prime time?

prime editing

Prime editing, a mightier version of CRISPR/Cas9 technology, has been part of rigorous research and development in recent years. Now, U.S. regulators have greenlit the first-ever clinical trial for this technology.

Massachusetts-based Prime Medicine received the go-ahead from the U.S. Food and Drug Administration (FDA) after preclinical data showed that its candidate was able to correct mutations in chronic granulomatous disease (CGD).

CGD is a rare condition and affects around one in 200,000 people worldwide. It is caused by mutations in any of the six genes that code for the molecule nicotinamide adenine dinucleotide phosphate (NADPH), which is responsible for carrying electrons within cells. White blood cells called phagocytes don’t function properly, and as a result, they fail to protect the body from bacterial and fungal infections.

Prime’s PM359 could put an end to the lifelong need for patients to take antibiotics and antifungals to prevent infections. The drug has moved quickly through the preclinical stages, considering that the concept behind prime editing was only described for the first time ever in a research paper, a mere five years ago.

Also called search-and-replace genome editing, the technology “substantially expands the scope and capabilities of genome editing, and in principle can correct up to 89% of known genetic variants associated with human diseases,” according to the paper published in the National Library of Medicine.

Table of contents

    How does prime editing work?

    While the mechanism is rooted in CRISPR/Cas9 genetic scissors, Kerstin Pohl, senior manager of Cell & Gene Therapy and Nucleic Acids at SCIEX, explained that prime editing uses a fusion protein that consists of a Cas9 enzyme and another enzyme called reverse transcriptase (RT), a ribonucleic acid (RNA) molecule, and the prime editing guide RNA (pegRNA), to correct mutations. 

    “Like traditional CRISPR/Cas9, it uses a guide RNA to direct a Cas9 protein to a precise location within the genome… The guide RNA contains an additional sequence on the end that acts as a template for the RT,” said Ashley Jacobi, director of Applications and Market Development at Integrated DNA Technologies (IDT). “When a cell tries to repair the cut in the DNA induced by the Cas9 protein, it can now incorporate the new length of DNA that was ‘written’ by the RT.”

    But unlike traditional CRISPR/Cas9 that cuts both strands of the DNA helix and gives no instruction to the cell on how to repair this cut, Jacobi pointed out that prime editing cuts only one strand of DNA, like with base editing, another offshoot of CRISPR that moved to the clinic last year. It can also create more precise and versatile edits.

    “It is not limited to random insertions and deletions like traditional CRISPR, or single base changes like base editing,” said Jacobi.

    While CRISPR/Cas9 is often referred to as genetic scissors, prime editing is likened to a word processor as it searches for and replaces disease-causing gene sequences at their exact location, much like what the computer program does with incorrect text.

    However, Pohl revealed that pegRNAs are challenging in design. These are synthetic RNA molecules that range from around 120 to 250 nucleotides in length. For this RNA to work as a scaffold for the Cas9-reverse transcriptase fusion protein, a high degree of complementary sequence is needed. But the resulting secondary structures could interfere with pegRNA function and pose a threat to how its purity is assessed, which is a quality control requirement for drugs.

    Prime editing could treat genetic disorders, but is it a cure?

    CGD isn’t the only disease that can be addressed with the help of prime editing. While CASGEVY, the first-ever CRISPR drug to be approved, is used to treat genetic blood disorders like sickle cell disease and beta-thalassemia, prime editing could take its word processing capabilities to target different kinds of genetic disorders.

    “Prime editing can allow scientists to fix mutations that can’t be repaired by other CRISPR systems. For genetic disorders with multi-base insertions, deletions, or substitutions, prime editing could be used to go in and precisely change those mutations. This includes disorders such as cystic fibrosis, sickle cell anemia, and even some forms of cancer,” said Jacobi.

    Although Prime’s other indications have not hit the clinic yet, it does intend to treat a variety of diseases. This includes Wilson’s Disease, a genetic disorder that causes copper buildup, Fanconi anemia, a rare genetic blood disorder, cystic fibrosis, which is caused by clogged mucus in the lungs, and the nerve disorder Friedreich’s ataxia, to name a few.

    “With prime editing’s potential to correct a wide range of disease-causing genetic variations, the technology opens up a lot of exciting possibilities for the field.”

    Ashley Jacobi, director of Applications and Market Development at Integrated DNA Technologies

    While Prime Medicine, which seems to be the only biotech that has a fully drawn out pipeline based on prime editing technology, intends to treat a range of diseases, Jacobi thinks it could be a cure – at least in theory, it sounds like it. For instance, in cystic fibrosis, the deltaF508 CFTR mutation accounts for 70% of the cases. This is a three-base deletion that could be fixed by a carefully designed prime editing guide RNA, according to Jacobi.

    “There’s still a lot of work to be done, but the basic mechanism is there,” she said.​​

    Tackling cost and design hurdles

    However, the technology is not without its drawbacks. As this technology is still in its early stages, Jacobi said that “it’s important to acknowledge that there are many areas needing improvement, especially with respect to editing efficacy, delivery, and safety.”

    Depending on the site of the edit, each new edit requires careful design and testing of the guide RNA, because the ideal design parameters are not fully understood. And since the prime editing protein is quite large in size, its delivery into tissues needs to be worked out. Plus, safety concerns exist, even though it is claimed to be more precise than CRISPR/Cas9.

    “Prime editing utilizes a single-stranded DNA break, resulting in rare instances of unintended insertions at on-target sites, unlike that of CRISPR-Cas9’s double-stranded breaks. Although this improves prime editing’s safety profile, it does not negate its risks,” said Jacobi.

    And then there are soaring manufacturing costs to consider. CASGEVY’s whopping $2.2 million price has made many Americans with sickle cell disease and beta-thalassemia wary of the treatment, as they are worried insurance won’t cover the entire cost of care. Although a long way to go, if prime editors are approved, this would be the case for drugs leveraging the technology as well.

    To address the costs of gene editing, a task force convened by the Innovative Genomics Institute, a non-profit run by CRISPR pioneer Jennifer Doudna, has been set up. The project is a first step toward developing a roadmap to cut manufacturing costs.   

    And while scientists are yet to iron out the kinks with regards to drug delivery, the FDA nod gives hope to many people living with genetic disorders.

    Jacobi said: “With prime editing’s potential to correct a wide range of disease-causing genetic variations, the technology opens up a lot of exciting possibilities for the field. It will allow researchers to optimize how they fix the mutations, get them delivered to the correct location in the body, and assess the safety of the tool. It will also allow the field to identify and overcome unforeseen barriers in patient treatment.”

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