A team at EPFL’s Laboratory of Protein Design & Immunoengineering (LDPI), led by Professor Bruno Correia, working with Dominik Niopek’s lab at Heidelberg University Hospital and the BioQuant Center, Heidelberg, Germany, have designed a protein (AcrX in short), using computational approaches, that can control CRISPR genome-editing in human cells. The study just appeared in the journal Nature Chemical Biology.
Acr (Anti-CRISPR) proteins are powerful tools to control CRISPR-Cas technologies. However, the available Acr repertoire is limited to naturally occurring variants. In order to make the breakthrough, the team had to think laterally. “Our artificial protein is an upgrade to proteins existent in nature”, says Prof. Correia of EPFL’s School of Engineering (STI). “We went back to the drawing board and applied structural design principles to enhance the natural version of the protein. In other words, we designed this molecule by simulating many possible variants in the computer and identified the most promising ones.”
As a synthetic protein, AcrX can fulfill functions that are beyond the reach of naturally occurring proteins. In this case, it acts like a pause button, giving scientists greater control over CRISPR-Cas9. “Inhibitory proteins occur in nature, but the artificial one we’ve developed is much more effective. It can, for instance, fully block CRISPR activity an avoid off-target editing, thereby making genome editing much safer. This might, in the future, become highly relevant for therapeutic genome editing directly within patients with genetic disorders” adds Correia.
CRISPR-Cas molecular scissors
CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. Put simply, it is a genome-editing tool that works like a pair of high-precision molecular scissors, snipping away target DNA that can then be discarded or replaced with other genetic material. But it comes with a catch: It is typically difficult to stop CRISPR’s editing activity after inserting it into cells or a living organism. “When CRISPR-Cas9 gets to work inside cells, it can have potentially toxic or disease-causing off-target effects,” explains Zander Harteveld, a doctoral assistant at the LDPI. “The likelihood of these off-target effects increases with time. That’s why it’s so important to have a pause button.” The AcrX protein serves precisely that purpose.
The new protein is the result of 18 months of research. The next step for the team is to optimize the delivery of the protein in cells and see how it can work in vivo. Ultimately, their discovery could pave the way for safer, more effective and better-targeted gene therapies.