Newly Discovered CRISPR System Shuts Down Cells to Thwart Infection

Although CRISPR-Cas9 has made significant waves since Jennifer Doudna and Emmanuel Charpentier discovered it, the overall gene editing field is young. Researchers around the globe are still deciphering the basic structure of these systems, what makes them tick and how we can leverage them for human health.

Now, an international team from the U.S. and Germany has added to that knowledge with the discovery of a new CRISPR system that could enable the “programming” of cells—an ability that has implications for cancer therapeutics, genome editing, microbiomes, and much more.

Six years in the making, the tandem papers published in Nature late last week, describe the structure and function of the newly discovered CRISPR-Cas12a2 system. Unlike better-known CRISPR systems that deactivate foreign genes to protect cells, CRISPR-Cas12a2 shuts down infected cells to thwart infection.

“With this new system, we’re seeing a structure and function unlike anything that’s been observed in CRISPR systems to date,” said corresponding author Ryan Jackson, assistant professor at Utah State University.

The element that sets Cas12a2 apart from others is its binding process and defense mechanism. For example, the well-known CRISPR-Cas9 system binds to target DNA and cuts it, like molecular scissors, to shut off the targeted gene. However, Cas12a2 binds to RNA, and when it does, it undergoes major structural changes.

Targeting RNA triggers collateral nucleic acid cleavage that degrades RNA, single-stranded DNA, and double-stranded DNA. This activity leads to cell arrest, presumably by damaging DNA and RNA in the cell, which impairs growth.

Using cryo-electron microscopy, Jackson and his team successfully demonstrated CRISPR-Cas12a2’s RNA-triggered degradation of single-stranded RNA, single-stranded DNA and double-stranded DNA, resulting in a naturally occurring defensive strategy called abortive infection.

“Incredibly, Cas12a2 nucleases bend the usually straight piece of double-helical DNA 90 degrees to force the backbone of the helix into the enzymatic active site, where it is cut,” said Jackson. “It’s a change in structure that’s extraordinary to observe.”

Normally, bacteria and archaea use the abortive infection defense mechanism to limit the spread of viruses and other pathogens. To find it in a CRISPR system is unique.

“A few other CRISPR-Cas systems work in this way. However, a CRISPR-based defense mechanism that relies on a single nuclease to recognize the invader and degrade cellular DNA and RNA has not been observed before,” said Oleg Dmytrenkom a postdoc at the Würzburg Helmholtz Institute for RNA-based Infection Research (HIRI), who collaborated with USU on the study.

As proof-of-principle, the researchers showed Cas12a2 can be used for molecular diagnostics and direct detection of RNA biomarkers with a limit of detection comparable with existing technologies.

In their study, the researchers say they envision a variety of applications beyond detection of RNA for Cas12a2, including the programmable shaping of microbial communities, cancer therapeutics and counterselection to enhance genome editing.

“If Cas12a2 could be harnessed to identify, target and destroy cells at the genetic level, the potential therapeutic applications are significant,” he says. “We’re just scratching the surface, but we believe Cas12a2 could lead to improved and additional CRISPR technologies that will greatly benefit society.”