Is the Prime Edit ready for prime time?

Prime editing, a more powerful version of CRISPR/Cas9 technology, has been the subject of intense research and development in recent years, and now U.S. regulators have given the green light for the first clinical trial of the technology.

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

CGD is a rare disease, affecting about one in 200,000 people worldwide. It is caused by mutations in one of the six genes that encode the molecule nicotinamide adenine dinucleotide phosphate (NADPH), which is responsible for transporting electrons within cells. White blood cells, called phagocytes, do not function properly and therefore cannot protect the body from bacterial and fungal infections.

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

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

How does Prime editing work?

The mechanism is based on the genetic scissors CRISPR/Cas9. Kerstin Pohl, Senior Manager for Cell and 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 molecule (RNA) and the prime editing guide RNA (pegRNA) to correct mutations.

“Like traditional CRISPR/Cas9, a guide RNA is used to direct a Cas9 protein to a precise location in the genome… The guide RNA contains an additional sequence at the end that serves as a template for the RT,” said Ashley Jacobi, director of applications and market development at Integrated DNA Technologies (IDT). “When a cell attempts to repair the cut in the DNA caused by the Cas9 protein, it can now incorporate the new length of DNA ‘written’ by the RT.”

But unlike traditional CRISPR/Cas9, which cuts both strands of the DNA helix and doesn’t give the cell instructions on how to repair that cut, Jacobi says prime editing cuts only one strand of DNA, as does base editing, another offshoot of CRISPR that entered the clinic last year. Prime editing can also make more precise and versatile edits.

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

While CRISPR/Cas9 is often referred to as genetic scissors, Prime Editing is similar to a word processor because it searches for and replaces disease-causing gene sequences at the exact location, much like the computer program does with faulty text.

However, Pohl pointed out that developing pegRNAs is challenging. These are synthetic RNA molecules that are about 120 to 250 nucleotides long. In order for this RNA to act as a scaffold for the Cas9 reverse transcriptase fusion protein, a high degree of sequence complementarity is required. However, the resulting secondary structures could impair the function of the pegRNA and jeopardize the assessment of its purity, which is a prerequisite for drug quality control.

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

CGD is not the only disease that can be treated using prime editing. While CASGEVY, the first approved CRISPR drug, is used to treat genetic blood disorders such as sickle cell anemia and beta thalassemia, prime editing could use its text processing capabilities to treat other types of genetic diseases.

“Prime editing allows scientists to fix mutations that cannot be repaired using other CRISPR systems. For genetic disorders involving insertions, deletions or substitutions of multiple bases, prime editing could be used to precisely alter these mutations. These include diseases such as cystic fibrosis, sickle cell anemia and even some cancers,” said Jacobi.

Although Prime’s other indications are not yet used in the clinic, the drug is intended for the treatment of a number of diseases. These include Wilson’s disease, a genetic disorder that causes copper deposits, Fanconi anemia, a rare genetic blood disorder, cystic fibrosis, caused by clogged mucus in the lungs, and the nerve disease Friedreich’s ataxia, to name a few.

“Because prime editing has the potential to correct a wide range of disease-causing genetic variations, the technology opens up many exciting possibilities in this field.”

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

While Prime Medicine, apparently the only biotech with a fully developed pipeline based on prime editing technology, aims to treat a range of diseases, Jacobi believes it could be a cure – at least in theory, that’s what it sounds like. In cystic fibrosis, for example, the deltaF508 CFTR mutation accounts for 70% of cases. It’s a three-base deletion that Jacobi says could be fixed 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.

Overcoming cost and design hurdles

However, the technology also has its drawbacks. Since the technology is still in its early stages, Jacobi says it is “important to recognize that there are many areas where improvements are needed, particularly in terms of the effectiveness, delivery and security of processing.”

Depending on the editing location, each new edit requires careful design and testing of the guide RNA, as the ideal design parameters are not yet fully understood. And because the main editing protein is quite large, its delivery into the tissue needs to be worked out. There are also safety concerns, despite it being supposedly more precise than CRISPR/Cas9.

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

And then there are the rising manufacturing costs to consider. CASGEVY’s hefty $2.2 million price tag has made many Americans with sickle cell disease and beta thalassemia wary of the treatment, fearing that insurance won’t cover the full cost of treatment. Although there’s still a long way to go, if major publishers are approved, drugs using this technology would too.

To reduce the cost of genome editing, a working group has been established at the Innovative Genomics Institute, a nonprofit organization led by CRISPR pioneer Jennifer Doudna. The project is a first step toward developing a plan to reduce manufacturing costs.

Although scientists have yet to find a solution to the problems associated with administering the drugs, the FDA’s approval offers hope to many people with genetic disorders.

Jacobi said: “Because prime editing can 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 the way they fix the mutations, deliver them to the right place in the body, assess the safety of the tool, and identify and overcome unforeseen obstacles in patient treatment.”

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