Is prime editing ready for prime time?

Prime editing, a more powerful version of CRISPR/Cas9 technology, has been part of rigorous research and development in recent years. Now, US regulators have given the green light to the first-ever clinical trial for this technology.

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

CGD is a rare condition, affecting approximately one in 200,000 people worldwide. It is caused by mutations in one of six genes that code for the molecule nicotinamide adenine dinucleotide phosphate (NADPH), which is responsible for transporting electrons in cells. White blood cells called phagocytes do not function properly and as a result they fail to protect the body against bacterial and fungal infections.

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

The technology, also called find-and-replace genome editing, “substantially expands the scope and capabilities of genome editing, and could in principle correct up to 89% of known genetic variants associated with human disease,” it said article published in the National Library of Medicine.

How does prime editing work?

Although the mechanism has its origins in the 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 consisting of a Cas9 enzyme and another enzyme called reverse transcriptase (RT). ), a ribonucleic acid (RNA) molecule, and the main 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 extra sequence at 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 break in DNA induced by the Cas9 protein, it can now take up the new length of DNA ‘written’ by the RT.”

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

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

Although CRISPR/Cas9 is often called genetic scissors, prime editing has been likened to a word processor that finds and replaces disease-causing gene sequences at their precise location, just as a computer program does with incorrect text.

However, Pohl revealed that pegRNAs pose a design challenge. These are synthetic RNA molecules with a length of approximately 120 to 250 nucleotides. For this RNA to act as a platform for the Cas9 reverse transcriptase fusion protein, a high degree of complementary sequence is required. But the resulting secondary structures can disrupt pegRNA’s function and threaten the way its purity is assessed, which is a quality control requirement for drugs.

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

CGD is not the only disease that can be tackled using prime editing. While CASGEVY, the first CRISPR drug ever approved, is used to treat genetic blood disorders such as sickle cell disease and beta thalassemia, Prime Editing could use its word processing capabilities to target different types of genetic disorders.

“Prime editing allows scientists to repair mutations that cannot be repaired by other CRISPR systems. For genetic disorders involving multi-base insertions, deletions or substitutions, prime editing could be used to precisely change those mutations. This includes conditions such as cystic fibrosis, sickle cell anemia and even some forms of cancer,” Jacobi said.

While Prime’s other indications have not yet entered the clinic, it plans 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 blocked 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 many exciting possibilities for the field.”

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

While Prime Medicine, which appears to be the only biotech with a fully comprehensive pipeline based on prime editing technology, plans to treat a range of diseases, Jacobi thinks it could be a cure – at least in theory it sounds that way. For example, in cystic fibrosis, the deltaF508 CFTR mutation is responsible for 70% of cases. This is a three-base deletion that Jacobi believes can be overcome by a carefully designed prime editing guide RNA.

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

Addressing cost and design hurdles

However, the technology is not without disadvantages. Because this technology is still in its early stages, Jacobi said that “it is important to recognize that there are many areas that need improvement, especially regarding machining effectiveness, delivery and safety.”

Depending on the location of the operation, each new operation requires careful design and testing of the guide RNA, as the ideal design parameters are not fully understood. And since the primary processing protein is quite large, its delivery into the tissues must be elaborated. Additionally, there are safety concerns even though it is claimed to be more accurate than CRISPR/Cas9.

“Prime editing uses a single-stranded DNA break, resulting in rare cases of unintended insertions at target sites, unlike the double-stranded breaks of CRISPR-Cas9. While this improves the safety profile of prime editing, it does not eliminate its risks,” Jacobi said.

And then there are rising production costs to take into account. CASGEVY’s whopping $2.2 million price tag has made many Americans with sickle cell disease and beta-thalassemia wary of the treatment, worried that insurance won’t cover the full cost of care. While there is still a long way to go, if the editors are approved, this would also be the case for drugs using the technology.

To address the costs of gene editing, a task force convened by the Innovative Genomics Institute, a nonprofit led by CRISPR pioneer Jennifer Doudna, has been created. The project is a first step towards developing a roadmap to reduce production costs.

And while scientists have yet to solve the problems surrounding drug delivery, the FDA nod gives hope to many people living with genetic conditions.

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

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