Learning to control microglia using CRISPR

The study suggests ways to target microglia, shown here in pink among neurons, in order to treat brain diseases such as Alzheimer’s disease. ART-ur / Shutterstock

Genetic research suggests that cells called microglia play a key role in brain diseases such as Alzheimer’s disease. Microglia help maintain the brain by clearing out damaged cells and infectious agents. They're also supposed to get rid of the plaques associated with dementia. Genetic changes may lead to disease by causing microglia to malfunction. But how individual genes affect microglial function isn’t well understood.

CRISPR-based tools could help yield insights. These techniques allow researchers to turn specific genes on or off. CRISPR systems typically rely on RNA delivered into cells using viruses, but this has been challenging in mature microglia. One way to circumvent the problem would be to introduce all the needed CRISPR components into stem cells and then turn the cells into microglia. But conventional methods for converting stem cells to microglia take weeks to months.

An NIH-funded team of researchers, led by Drs. Li Gan of Weill Cornell Medicine and Martin Kampmann at the University of California, San Francisco, set out to engineer human stem cells that could more quickly be converted to microglia-like cells for study. They described their work on August 11, 2022, in Nature Neuroscience.

The team developed a method to generate microglia-like cells from stem cells in eight days. They confirmed that these cells, dubbed iTF-Microglia, behaved like ordinary human microglia. They then introduced complete CRISPR systems into the stem cells before converting them into iTF-Microglia. This created iTF-Microglia in which genes could be turned off or on and studied.

Using this approach, the team was able to identify genes that affected microglial survival and activation. They also found genes that affected the microglia’s ability to engulf nerve cell debris, a key function of microglia in the brain. Some of the genes have been associated with neurodegenerative diseases. These findings now provide further potential drug targets. 

The team also identified nine distinct microglial states based on gene activity, or expression, patterns. These states reflected the diversity of microglial states observed in human brains. Turning certain genes on or off could shift microglia from one state to the other.

Notably, one of these states was characterized by high expression of the gene for osteopontin. Microglia associated with Alzheimer’s disease have been shown to have high osteopontin levels. Turning off one gene, MAPK14, increased the number of microglia in this high-osteopontin state. Turning off another gene, CSF1R, reduced the number in this state, as did treatment with a drug that blocks CSF1R.

These findings give insight into how genetic variations might contribute to Alzheimer’s and other diseases of the brain. Therapies could target these genes to treat disease by shifting microglia from a pathogenic state to a healthy state.

“Now, using the new CRISPR method we developed, we can uncover how to actually control these microglia, to get them to stop doing toxic things and go back to carrying out their vitally important cleaning jobs,” Kampmann says. “This capability presents the opportunity for an entirely new type of therapeutic approach.”

—by Brian Doctrow, Ph.D.