Study: CRISPR-Cas9 Gene Editing Could Increase Cancer Risk

The scientific research community has been extremely careful since Jennifer Doudna and Emmanuelle Charpentier debuted the CRISPR-Cas9 gene editing system in 2012. Doudna herself called for an immediate moratorium to ensure the landmark discovery was used only when safe and appropriate.

A decade later, CRISPR-Cas9 has been utilized successfully, especially in gene therapy; but, a new report from researchers at Boston Children’s Hospital brings to light a potential, previously undiscovered danger of gene-editing.

In a study published in Nature Communications, Roberto Chiarle, MD, and colleagues show, for the first time, that CRISPR-Cas9 can cause large rearrangements of DNA through a process called retrotransposition—which is known to trigger cancer. Fortunately, retrotransposition events caused by CRISPR were uncommon, only occurring 5 to 6 percent of the time in the study’s experimental model.

Still, when all it takes to initiative a tumor is one cell with a transposition event, the magnitude of CRISPR edits is concerning. In most gene therapies, CRISPR is used to target a few million cells before the edited versions are retuned to the patient.  

While the researchers studied classical CRISPR/Cas9 in multiple human cell lines, Chiarle stressed that the study is purely experimental at this point.

“We need to determine how often retrotransposition happens in clinical trials of CRISPR gene therapies,” the pathology researcher said.

Study co-author Jianli Tao, also in the pathology department of Boston Children’s Hospital, refined an existing test called PolyA-seq, and set up the experimental system to validate it. The test identifies retrotransposition events involving LINE-1, the most common “jumping gene,” or mobile element.

“We think this test could help detect these events more reliably, and it may be more cost-effective than the method that’s commercially available,” said Tao.

Safer alternatives

During a retrotransposition event, DNA sequences known as “jumping genes” move from one location in the genome to another. Using enzymes, they replicate and create a break in both strands of the DNA double helix, where they insert themselves. While this can be—and is often—harmless, jumping genes and the act of retrotransposition have been repeatedly linked to cancer and other diseases.

By nature, CRISPR also introduces double-strand breaks in DNA, thereby increasing the chances of retrotransposition. Now, Chiarle, Tao and their colleagues have found a safer alternative that is effective without breaking the double helix.

The scientists discovered that retrotransposition is much rarer during base editing—a newer, more precise technique that chemically changes just one base of the genetic code without causing a double-strand break in DNA. With this technique, retrotransposition events were detected less than 0.01 percent of the time.

The harmful events were also less frequent during prime editing, an advanced technique that enables targeted insertions, deletions and all 12 possible base changes.

“We demonstrate that both base editors and prime editors are much safer and are associated with very low retrotransposition events compared with CRISPR/Cas9,” said Chiarle.

Safety toolbox

At this time, the researchers suggest that tests for retrotransposition be added to safety testing for CRISPR/Cas9 editing systems. Current test technologies either sequence small stretches of DNA to ensure that the desired gene has been added or deleted in the right place, or are designed to detect small gene rearrangements—they don’t look for large rearrangements caused by retrotransposition.

“We hope our findings will encourage investigators using CRISR/Cas9 to include a check for insertion of [jumping genes],” concluded Chiarle. “CRISPR is really a game-changer in genetic therapy, so it’s very important to know exactly what it does to ensure its safety.”