Nanobodies could help CRISPR turn genes on and off

The CRISPR genetic tool has been compared to molecular scissors for its ability to cut and replace genetic code in DNA. But CRISPR has a potential that could make it useful in addition to genetic repairs. “CRISPR can precisely locate specific genes,” said Lacramioara Bintu, an assistant professor of bioengineering at Stanford. “What we did was attach CRISPR to nanobodies to help it perform specific actions when it reached the correct spot on the DNA.”

Her lab recently used this combo technique to transform CRISPR from gene editing scissors into a nanoscale control device that can turn on and off specific genes, such as a light switch, to start or stop the flow of some health-related protein in a cell. . .

“There are a lot of things you can’t fix with scissors,” says Bintu. The new technique that her team describes in the magazine Nature Communications could enable researchers to explore new therapeutic applications in epigenetics – the study of how genes behave in cells.

As Bintu explains, every cell in the human body has the same DNA – a full complement of genes – but not every gene is turned on in every cell. Some cells have certain genes that tell the cell to produce specific proteins. Others turned those genes off, but others turned on. Sometimes, as with genetic diseases, things go wrong with this switch. The new tool from the Bintu lab has the potential to correct those errors.

The new tool is more complicated than scissors, because ordinary CRISPR cannot switch genes on and off in a controlled way without breaking the DNA. To make changes without damaging DNA, CRISPR requires help from other large, complex proteins known as “effectors.” With the new combo tool, CRISPR finds the right gene and the effector can flip the switch.

“But these effector molecules are usually too large to easily release into a cell for therapeutic use,” says Ph.D. student Mike Van, lead author of the article. Complicating matters further is that different effectors are usually used in combination to efficiently regulate specific cell behaviors, making the combination of CRISPR effectors even larger, and thus more difficult to produce and deliver.

To get around this roadblock, Bintu’s team turned to smaller proteins known as nanobodies. Nanobodies do not act as stand-ins for the effectors. Instead, they act like little hooks that snare the needed effectors already swimming around the cell. Choose the right nanobody and it will recruit the right effector for the shift job.

The new technique could be used to correct epigenetic defects without the need to combine CRISPR with large effectors. “The cells already have these proteins,” explains Bintu. “We thought: why are we reattaching them? Let’s use nanobodies for that.”

At this point, the technique is in the proof-of-concept phase. The next step is for the team to search millions of potential nanobodies and begin to figure out how to link them to CRISPR to address specific epigenetic malfunctions.

“We just came up with a method to test hundreds of thousands at a time,” said Bintu, who hopes to further develop the technique in future experiments.

Provided by Stanford University School of Engineering