How a genetic 'CopyCatcher' could open the door to CRISPR-based precision gene therapy

DNA genomics precision medicine
With help from a genetic sensor called "CopyCatcher," scientists at the University of California, San Diego showed that CRISPR-based gene therapy is possible. (Pixabay)

Gene therapies such as Novartis’ spinal muscular atrophy treatment Zolgensma deliver a surrogate copy of a gene to replace a dysfunctional one in the body. The CRISPR gene editing tool could offer an alternative strategy—one that could allow for a mutated gene to be fixed on site. But scientists aren’t sure whether such a technique, known as “gene drive,” would work at scale.

Researchers at the University of California, San Diego (UCSD) say they may have found a way to make CRISPR efficient in gene therapy. They have developed a technology called “CopyCatcher,” which can detect and quantify events in which a genetic element is copied precisely from one chromosome to another during CRISPR-based gene editing.

In fruit flies, CopyCatcher revealed unexpectedly high rates of gene conversion, according to results published in Nature Communications. With help of the new tool and DNA screening, the team also identified the c-MYC gene as an inhibitor of genetic copying in human embryonic cells. The researchers said the findings lay the groundwork for developing CRISPR-based gene therapy for humans.

The promise of CRISPR-based gene drives is that one chromosome bearing the drive can cut the other chromosome, which uses the drive as a template to repair the damage. UCSD used CopyCatcher to measure the efficiency of such a system in living animals.

CopyCatcher carries a highly sensitive “detector” gene that produces fluorescent proteins only if the target genetic element copies itself onto a sister chromosome, allowing investigators to detect and quantify gene conversion.

In fruit flies, the frequency of gene conversion was unexpectedly high, at 30% to 50% of cells in the targeted tissues of the eye and thorax, the team reported.

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But the rates of chromosome copying dropped sharply to just 4% to 8% of cells in human cells. That may be because mammalian chromosomes don’t typically engage in chromosome pairing but rely instead on a different mechanism to fix DNA cuts. The researchers showed they could use certain techniques to improve copying, suggesting that human cells might be induced to perform efficient gene conversion.

By using a genetic screen, the team identified several factors affecting how DNA selects a repair pathway. The gene c-MYC emerged as a prime inhibitor of templated gene conversion. Cutting the expression of c-MYC by half increased the production of fluorescence marker expression by 2.5-fold in human embryonic cells compared with control cells, the team showed.

If high-efficiency gene editing could be achieved in human cells, CRISPR-based gene therapies could be developed to treat a variety of genetic disorders including blood diseases, hearing loss, spinal muscular atrophy, congenital heart defects and others, the researchers suggested.

“These studies provide a clear proof of principle for a new type of gene therapy in which one copy of a mutated gene could be repaired from a partially intact second copy of the gene,” Ethan Bier, Ph.D., the study’s senior author, said in a statement. “The need for such a design occurs in genetic situations with patients with inherited genetic disorders, if their parents were carriers for two different mutations in the same gene.”

For future studies, the researchers plan to use CopyCatcher to identify additional factors that can be manipulated to push the choice of DNA repair toward the chromosome-pairing mechanism. That could improve the efficiency of CRISPR-based editing, they believe.