A Revolution in CRISPR Technology – Precisely Targeting Every Gene with a New Enzyme

Engineers at Duke University have developed a new method. Whereas original CRISPR gene-editing technology could target only part of the human genome —just 12.5%—the new approach reaches almost every gene, making it possible to target and treat a wider range of diseases.

Nature Communications published the study, which also involved collaborators at Harvard University, the Massachusetts Institute of Technology, the University of Massachusetts Medical School, the University of Zurich, and McMaster University.

Pranam Chatterjee, assistant professor of biomedical engineering at Duke University, said, “With this new tool, we can target almost 100% of the genome with much greater precision,” he explained.

A Reminder of the CRISPR-Cas System

CRISPR-Cas uses RNA molecules and CRISPR-associated (Cas) proteins to enable bacteria to target and destroy invading viruses' DNA. It is a bacterial immune system. Since this gene-editing technology was discovered, researchers have raced to develop new CRISPR systems for gene therapy and genome engineering applications.

CRISPR technology, both for its achievements to date and its potential to change the future, was recognized with the 2020 Nobel Prize in Chemistry.

The team explored the new tool's potential therapeutic use for genetic diseases that cannot be treated with standard CRISPR systems. Initial tests focused on Rett syndrome, a progressive neurological disorder seen particularly in young women and caused by one of eight different mutations in a specific gene.

Their second test involved Huntington's disease, a rare inherited neurological disorder causing degeneration of brain neurons. Using the new technology, the team modified previously inaccessible mutations and offered potential treatment opportunities for both diseases.

How Do Conventional CRISPR and the New Enzyme Work?

During genome editing, Cas proteins use two important components. The first is an RNA molecule directing the enzyme to a specific DNA sequence. The second is a short DNA sequence immediately following the target sequence, required for Cas binding and called the protospacer adjacent motif (PAM). These components help guide Cas proteins accurately and effectively to the target DNA sequence.

When the guide RNA identifies its complementary target DNA sequence and the Cas enzyme binds to the adjacent PAM sequence, the enzyme makes a cut in the DNA. This initiates the desired changes in the genetic material. The most common CRISPR-Cas system is the Cas9 system from Streptococcus pyogenes (SpCas9), which requires two consecutive guanine bases (GG).

In previous work, Chatterjee and colleagues used bioinformatics tools to discover and engineer new Cas9 proteins, including Sc++, requiring only a single guanine-base PAM to make a cut. This allowed researchers to edit approximately 50% of all DNA sequences.

Meanwhile, Chatterjee's Harvard collaborators, led by Benjamin Kleinstiver, an assistant professor at Harvard Medical School, developed a separate variant, SpRY. Although SpRY could bind to any of the four DNA bases forming a PAM, it had a much stronger preference for adenine and guanine.

Because both systems had drawbacks, the group decided to combine their best features in a new variant called SpRyc.

Although SpRYc cuts target DNA sequences more slowly than its predecessors, it can edit specific DNA regions more effectively than conventional enzymes.

Conclusion and Commentary

SpRYc is opening the door to a new era in gene editing. This innovative enzyme's potential matters not only in the laboratory but also for translation into clinical applications. Its improved efficiency and high precision could play a critical role in shaping the future of gene therapy. As advances open new possibilities for treating genetic diseases, exploring SpRYc's full capabilities represents an exciting journey for science.