April 9 (UPI) — Researchers developed a way to speed up analysis of CRISPR’s edits to DNA from one at a time over several weeks to tens of thousands simultaneously.
UCLA researchers figured how to quickly monitor the outcome of gene edits using the tool, called Clustered Regularly Interspaced Short Palindromic Repeats. Their research was published Monday in Nature Genetics journal.
“For several years, scientists have used CRISPR to cut many genes at one time,” lead author Leonid Kruglyak, chairman of human genetics at the David Geffen School of Medicine at UCLA, said in a press release. “But there was a lack of CRISPR methods to edit many genes at once. Our lab is the first to develop a large-scale technique for achieving this in cells structured like human cells.”
The UCLA team rapidly distinguished the most damaging genetic edits from the harmless with this process.
“We can now edit the genome in thousands of different ways, while observing positive or negative effects on cells,” said Kruglyak, who is also a Howard Hughes Medical Institute investigator. “Our ultimate goal is to help scientists zero in on the genetic culprit for a disease, leading doctors to a firm diagnosis and allowing patients to obtain the most effective treatment.”
CRISPR combines a scissor-like protein called Cas9 and a guide molecule that seeks a precise site in the genome. Then, Cas9 snips the DNA, which disables the targeted gene.
Scientists can edit a gene’s sequence and patch over the cut made by Cas9 with a new piece of DNA.
Researchers previously performed parallel edits in bacterial cells,which were organized differently than human cells, he said.
“For CRISPR to introduce edits to the genome properly, each cell needs to receive the right combination of guide and patch,” said Meru Sadhu, a postdoctoral researcher in Kruglyak’s lab. “Delivering the pairs correctly to thousands of cells at the same time posed a complicated scientific puzzle.”
To solve the problem, the researchers physically connected thousands of guides to their partner patches, forming a perfectly matched set for each cell.
In a test of a class of genetic mutations suspected to be harmful to cells, Kruglyak and Sadhu used yeast because cellular changes in response to gene alterations happen quickly and are easy to observe.
Researchers grew millions of cells inside a flask of fluid. CRISPR delivered a customized set of paired guides and patches to each cell — about 10,000 distinct mutations simultaneously. The guide and patches instructed CRISPR where to snip the gene and what edit to introduce.
This process distinguished cells that died or survived after four days.
“We were surprised to find that some genes believed to be essential for cell function actually aren’t,” Sadhu said. “In other genes, only a part of the protein is essential, while the rest can be chopped off and the cell will still survive.”