Humans have over 20,000 genes, making it very difficult to tease apart exactly which ones might be causing genetic diseases. To help probe this massive area of human health, researchers at McGill University modified a gene editing technique to turn specific repressed genes on while leaving the genome itself unchanged.
Being able to target gene expression with this level of precision could help us understand how to treat a wide variety of medical conditions, including cancers, mental health disorders, and autoimmune diseases like type 1 diabetes or rheumatoid arthritis.
The same genetic blueprint is carried by all cells in the body, and yet cells can specialize by turning selected genes on and off. One way that a cell can turn a gene off is by marking it with a tiny tag called a methyl group, a process that regulates a cell’s identity and function. Most times this is a good thing that keeps the body working the way it should.
But aside from cell specialization, altered DNA methylation is also associated with many medical conditions. Without a way to selectively control whether a gene is methylated or not, it was impossible for researchers to definitively test whether a specific methylation site might cause problems. Until now, existing methods either triggered unwanted changes in methylation across the genome or made artificial changes to DNA at the target location.
The new technique offers site-specific DNA demethylation in living cells as they divide in the lab, preserving everything else about the genetic code except for that tag. Their study was published in Nature Communications.
The team modified CRISPR/Cas9 genome editing technology to physically interfere with DNA methylation at a directed site. Right after a cell replicates a strand of DNA during cell division — creating a second set of DNA to pass one onto each of the new daughter cells — the fresh strand is untagged and is usually then methylated to maintain the parent strand’s pattern.
The demethylation technique uses a guide strand of RNA, written as a sequence of bases that reads as the complement to the target site. This allows it to specifically bind the target, and also provides a flexible way to target any site by updating the RNA sequence.
The guide strand pairs with an inactive Cas9 protein to physically block methylation, turning the gene back on. The authors didn’t find any off-target activity on other genes.
One drawback of this method is that it only works when cells are dividing, and they have to do so several times to dilute out the original pattern of gene expression. Culturing cells can lead to genetic drift over many generations, and this is also a time-intensive process.
That being said, this approach still has the potential to uncover specific methylation sites that trigger disease, revealing targets for treatment. For example, researchers may be able to find ways to turn up insulin production in people with type 1 diabetes, or activate regulators of cholesterol metabolism to reduce risk of cardiovascular disease.
Being able to ask these questions in the lab will ultimately help pinpoint better ways to treat a wide variety of genetic diseases in the clinic.