CRISPR changed everything. The gene-editing technology—in which researchers can precisely direct a set of molecular “scissors” to create genetic changes exactly where they want to—has transformed biomedical research and, increasingly, human medicine.
In the research space, one area where CRISPR has proved invaluable is generating mouse models. Mouse models have massively advanced our understanding of fundamental biology and provided the bedrock of improving therapies. CRISPR is the all-purpose tool that allows scientists to make those models, whether by precisely editing a gene involved in human disease or by introducing a gene for a fluorescent protein that lights up previously hidden biology. Cut, paste, done.
At least, that’s the theory. The practice is more complicated.
Even with the most painstakingly designed CRISPR protocol, edits don’t always happen the way researchers predict. The molecular scissors intended to target one gene may fail to make the correct edit—or may end up entirely elsewhere in the genome, changing the DNA in unexpected ways.
These off-target edits can be a major roadblock to getting meaningful results. To make sure that gene-edited mice have only the intended genetic edit, researchers cross them back to unedited mice over multiple generations, a process that can take a year or more.
For researchers at U of U Health, that process just got a lot smoother, powered by a creative combination of research cores.
Cheaper, better, faster CRISPR
Cores provide access to specialized expertise and top-of-the-line scientific equipment to labs across the U, allowing all scientists to take advantage of new research technologies. Now, a collaboration between three scientific cores has implemented a new pipeline for creating and quality-checking gene-edited mice, which cuts down the time involved by about a month.
Researchers can get a jumpstart on answering important questions, confident that the models they use are what they intended to make, while reducing the number of animals that are used—a central tenet of research at the U.
- First, in the Mutation Generation and Detection Core, experts help fine-tune the editing process to optimize the chances that CRISPR makes exactly the edits the researchers need. “We really try to do our best to make sure the edit goes on target,” explains Crystal Davey, PhD, director of the Mutation Generation and Detection Core as well as the Transgenic Mouse Core.
- Once the researchers make gene edits, the mice have their entire genomes sequenced in the DNA Sequencing Core. Once a time-consuming and costly endeavor, advanced sequencing technology recently implemented in the core now allows for a quick-turnaround result that’s more cost-effective than the current standard for mouse genotyping and requires fewer animals.
- Finally, the sequencing results are rapidly analyzed using software that’s been optimized to detect potentially harmful side-effect mutations. Computational tools developed in the Utah Center for Genetic Discovery Core check that the targeted gene is edited exactly as intended, scan the whole genome for large off-target edits, and return a result in as little as 20 minutes—faster and often cheaper than other sequencing strategies.
The end result? “We can make mice that have been difficult to make, we can make them faster, and we can be assured of our product at the end of the day,” explains James Cox, PhD, assistant vice president for cores infrastructure.
Moving forward
While the new pipeline is faster, cheaper, and more reliable than the previous standard, it’s not foolproof, Davey warns. The genome analysis doesn’t currently alert researchers of small-scale changes, which can also sometimes affect experimental results. But as researchers in the core sequence more mice and get a sense of the spectrum of genetic variation, they will aim to better understand which changes might be problematic. “It’s something I think we can work to improve,” Davey says.
Cox reiterates that communication between multiple research cores, each bringing their own expertise and resources to the table, is essential to this kind of science. “I want to cross-pollinate core directors so they can meet each other and talk about problems,” he says. “It’s about getting people to work together and do cool stuff together. That’s how we make really great science.”
