Researchers have discovered a way to program cells to inhibit CRISPR-Cas9 activity. “Anti-CRISPR” proteins had previously been isolated from viruses that infect bacteria, but now University of Toronto and University of Massachusetts Medical School scientists report three families of proteins that turn off CRISPR systems specifically used for gene editing. The work, which appears December 15 in Cell, offers a new strategy to prevent CRISPR-Cas9 technology from making unwanted changes.
“Making CRISPR controllable allows you to have more layers of control on the system and to turn it on or off under certain conditions, such as where it works within a cell or at what point in time,” says lead author Alan Davidson, a phage biologist and bacteriologist at the University of Toronto. “The three anti-CRISPR proteins we’ve isolated seem to bind to different parts of the Cas9, and there are surely more out there.”
CRISPR inhibitors are a natural byproduct of the evolutionary arms race between viruses and bacteria. Bacteria use CRISPR-Cas complexes to target and cut up genetic material from invading viruses. In response, viruses have developed proteins that, upon infection, can quickly bind to a host bacterium’s CRISPR-Cas systems, thus nullifying their effects.
Anti-CRISPR proteins are attractive experimentally because they offer one solution for preventing potential off-target effects. Research in mice has shown that such mistakes may be rare when using CRISPR-Cas9 technology, but even the occasional error could be a serious problem when being used therapeutically in humans.
“CRISPR-Cas9 in ancillary cells, tissues, or organs is at best useless and at worst a safety risk,” says co-author and collaborator Erik J. Sontheimer, a professor in the RNA Therapeutics Institute at the University of Massachusetts Medical School. “But if you could build an off-switch that keeps Cas9 inactive everywhere except the intended target tissue, then the tissue specificity will be improved.”
“Knowing we have a safety valve will allow people to develop many more uses for CRISPR,” says co-author Karen Maxwell, an assistant professor in biochemistry who is also at the University of Toronto. “Things that may have been too risky previously might be possible now.”
While the work will be of great interest to those studying gene editing and gene drives, Davidson’s team is also curious to follow up on the biology of how bacterial CRISPRs and viral anti-CRISPRs interact.
“We didn’t set out to find anti-CRISPRs, we were just trying to understand how phages incorporate themselves into bacterial genomes and stumbled onto something that I think will be important for biotechnology,” Davidson says.
“We were being observant and following a path that we didn’t know where it could lead, and it’s just been a very fun and exciting story.”
Learn more: An anti-CRISPR for gene editing
UMMS scientists develop multicolored labeling system to track genomic locations in live cells
“Most people are using CRISPR for editing genomes. We are using it to label DNA and track the movement of DNA in live cells,” said research specialist Hanhui Ma, PhD, who coauthored the study with Thoru Pederson, PhD, the Vitold Arnett professor of cell biology and professor of biochemistry and molecular pharmacology.
Knowing the precise location of genomic elements in live cells is critical to understanding chromosome dynamics because the genes that control our biology and health do so according to their location in 3-dimensional space, said Drs. Pederson and Ma. For a gene to be transcribed and expressed, it must be accessible on the chromosome. Where DNA is positioned in the crowded nucleus plays an important role in everything from embryonic development to cancer.
Current technologies, however, are only capable of following, at most, three genomic locations at a time in live cells. Labeling more sites requires that cells be fixed by bathing them in formaldehyde, thus killing them and making it impossible to observe how the chromosome’s structure changes over time or in response to stimuli.
To overcome this technological hurdle, Pederson and Ma turned to CRISPR/Cas9. To tag specific locations along the genome using the CRISPR/Cas9 complex, they created a Cas9 mutation that makes the nuclease inactive so it only binds to the DNA and doesn’t cut the genome. Once deactivated, the CRISPR/Cas9 element is ferried to a specific location on the genome by a guide RNA that can be programmed by the researchers.
New delivery method boosts efficiency of CRISPR genome-editing system
The genome-editing technique known as CRISPR allows scientists to clip a specific DNA sequence and replace it with a new one, offering the potential to cure diseases caused by defective genes. For this potential to be realized, however, scientists must find a way to safely deliver the CRISPR machinery and a corrected copy of the DNA into the diseased cells.
MIT researchers have now developed a way to deliver the CRISPR genome repair components more efficiently than previously possible, and they also believe it may be safer for human use. In a study of mice, they found that they could correct the mutated gene that causes a rare liver disorder, in 6 percent of liver cells — enough to cure the mice of the disease, known as tyrosinemia.
“This finding really excites us because it makes us think that this is a gene repair system that could be used to treat a range of diseases — not just tyrosinemia but others as well,” says Daniel Anderson, associate professor in MIT’s Department of Chemical Engineering and a member of MIT’s Koch Institute for Integrative Cancer Research and Institute for Medical Engineering and Science (IMES).
The University of Massachusetts is the five-campus public university system of the Commonwealth of Massachusetts.
The system includes four universities and a medical school. Across its campuses, the University of Massachusetts enrolls about 71,000 students.
The UMass system was ranked 56th in the world in 2010 by the Times World University Rankings. It was also ranked as the 19th best university in the world in the Times of London’s 2011 World Reputation Rankings. In 2012, the state of Massachusetts introduced $607 million in new bond funding to advance high-quality instructional and research facility projects throughout the UMass system.
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