Epigenetic editor silences prion proteins in brains of mice

Researchers in a laboratory established to find a treatment for prion diseases are announcing that they have made a step forward in mice. Collaborating with a genome-editing lab, they have developed a tool that can turn off expression of the prion protein in a mouse’s brain and that might work for other disease-related proteins (Science 2024, DOI: 10.1126/science.ado7082).

The tool is designed to overcome one of genetic medicine’s greatest challenges: getting therapies that can edit a cell’s genome into the cell where the editing is needed. Although scientists can manipulate cells in a dish fairly easily, delivering genetic therapies to the many types of cells in a living organism has more complications.

Prion diseases start when a protein in the brain misfolds into a form called a prion. Because one misfolded copy of the protein can recruit others into the same corrupted conformation, eventually the prions aggregate and kill neurons. This group of diseases is currently incurable—which is why, after a genetic prion disease killed Sonia Vallabh’s mother, Vallabh and her husband, Eric Minikel, founded a lab at the Broad Institute of MIT and Harvard dedicated to finding a cure for prion diseases (N. Engl. J. Med. 2020, DOI: 10.1056/NEJMp1909471). This project, in which her lab teamed up with Jonathan Weissman’s group at the Massachusetts Institute of Technology and the Whitehead Institute, is one of several strategies her lab is studying to reduce prion levels in the brain.

The new tool is an epigenetic editor. That means it does not change the sequence of DNA but rather the chemical modifications that indicate to a cell whether the DNA should be expressed. The researchers started with a CRISPR-based strategy that recruits a DNA-methylating enzyme to a portion of the prion gene. In effect, they found, methylating the DNA that encodes the prion protein leads a cell to bundle up that portion of the chromosome and stuff it into storage. This act prevents the protein from being produced—meaning it’s not available to misfold and aggregate.

But to work for patients, a tool must make it to the cells where prions wreak havoc. “It is a whole-brain disease, and we have to be realistic about that,” Vallabh says. “We’ll save the neurons we can reach.”

The problem is that the core protein in CRISPR approaches is much too bulky to fit into a viral vector, which is scientists’ best technology for delivering gene therapy to the brain. The new research uses a different strategy for targeting specific DNA sequences: compact zinc finger proteins. The researchers built a fusion protein from zinc fingers that bind to the prion gene and a ligand that recruits to a cell’s existing methyltransferase enzyme. The targeting worked, they found, but to activate the methyltransferase, they needed to also include part of a histone protein. The researchers dubbed the method CHARM: coupled histone tail for autoinhibition release of methyltransferase.

“The CHARM method is a beautiful example of how deeper basic science knowledge can be translated into a super-useful technology and a clinically relevant translational research tool,” says Mazhar Adli, a CRISPR and epigenetic researcher at Northwestern University who was not involved in the study. He adds that the technology “overcomes at least one of the formidable challenges” in silencing genes in the brain.

Indeed, the research team found that infecting mice with a virus carrying the CHARM editor led to lasting methylation of the prion gene and disappearance of the prion protein throughout the brain. Though the methods have not been compared directly, it seems as if one dose of CHARM could last longer and work more effectively than antisense oligonucleotides, which researchers are testing to suppress the translation of the prion protein.

Vallabh and Weissman both emphasize the difference between treating a mouse and testing in humans. CHARM will need to be optimized to target the human prion gene, engineered into a virus that targets human neurons, and most importantly, examined for safety and off-target effects before it’s ready for a single test in human patients. Vallabh expects to hear from many people who want a cure now, and she says it is always difficult to be the one to tell them medication doesn’t yet exist.

But the race to help patients—perhaps including herself—has taken on a different tenor now, Vallabh says. “It’s simultaneously very exciting to see good tools work and puts my heart in my throat.”