'Gentler' CRISPR sheds light on autoimmune disease

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UCSF scientists are developing a version of CRISPR that could help unravel the causes of autoimmune disease.

CRISPR is typically used to edit disease-causing gene mutations, but is increasingly being tapped for broader applications. The latest? Identifying sequences that activate genes, which could help unravel the causes of autoimmune disease.

While CRISPR shows great promise in the treatment of genetic disease, the genes it cuts out—those that code directly for proteins—only make up 2% of the human genome. The other 98% consists of regulatory gene sequences, including promoters, which switch on genes next to them, and enhancers, which activate genes that may sit far away from them in the genome.

When the balance of promoters and enhancers is out of whack, it can lead to disease. But it’s difficult to pinpoint just which regulators have a hand in causing disease, as specific regulators play a role in specific cells, under specific conditions.

Jacob Corn and Alexander Marson at the University of California, San Francisco, focused on T cells and the IL2RA protein, which tells T cells if they should step up or dampen an inflammatory response. If the enhancers that switch on IL2RA are faulty, the T cells don’t suppress inflammation, which could cause autoimmune disorders, such as Crohn’s and inflammatory bowel disease (IBD).

Corn and Marson used CRISPR activation, or CRISPRa, to home in on the IL2RA gene. This method uses a guide RNA to target sections of the genome, much like regular CRISPR, but instead of cutting them, it activates those sequences to see how they affect gene expression.

They created 20,000 guide RNAs for use with CRISPRa: "We essentially performed 20,000 experiments in parallel to find all the sequences that turn on this gene," said Marson, an assistant professor of microbiology and immunology at UC San Francisco, in a statement.

The team turned up several sequences that might be important for ILR2A expression, including a common genetic variant that was already linked to increased IBD risk but was not well understood. The findings are published in Nature.

"This starts to unlock the fundamental circuitry of immune cell regulation, which will dramatically increase our understanding of disease," Marson said.

The utility of CRISPR is growing by the day. Recently, UC San Diego researchers created a new version of CRISPR that targets RNA rather than DNA, which could be used to treat diseases caused by errant repeats in RNA sequences, including Huntington disease and a type of amyotrophic lateral sclerosis.

And scientists at eGenesis have deployed the gene-editing tool in the organ transplant field. By snipping out a family of viruses in the pig genome, they have overcome one obstacle in xenotransplantation, or using animal organs for human transplant.

The next step for the UCSF researchers is to modify their method so that it can screen for enhancers of many different genes at once.

"Not only can we now find these regulatory regions, but we can do it so quickly and easily that it's mind-blowing," said Corn, assistant adjunct professor of molecular and cell biology at Berkeley. "It would have taken years to find just one before, but now it takes a single person just a few months to find several."