Tools like CRISPR that cut DNA to alter its sequence are coming tantalizingly close to the clinic as a treatment for certain genetic diseases. But away from the limelight, researchers are increasingly excited about an alternative that leaves a DNA sequence untouched. These molecular tools target the epigenome, the chemical tags adorning DNA and its surrounding proteins that govern a gene’s expression and ultimate behavior.
A flurry of studies over the past few years in mice suggests that epigenome editing is a potentially safer and more flexible way to turn genes on or off than DNA editing. In one example described last month at a gene therapy meeting in Washington, DC, an Italian team reduced the expression of a gene in mice to lower the animals’ cholesterol levels for months. Other groups are exploring epigenome editing to treat everything from cancer to pain to Huntington’s disease, a deadly brain disorder.
Unlike DNA editing, where modifications are permanent and can include unintended outcomes, epigenomic modifications may be less likely to cause adverse off-target effects and can be reversed. They can also be more subtle, slightly increasing or decreasing a gene’s activity, rather than blasting it at full force or erasing it completely. “What’s exciting is that there are so many different things you can do with technology,” says Charles Gersbach, a longtime epigenome editing researcher at Duke University.
Adding or removing chemical tags on DNA and the histone proteins around which it wraps (see illustration, p. 1035) can either snuff out a gene or expose its DNA base sequence to other proteins that activate it. Some cancer drugs remove or add these chemical tags, but as disease fighters they have had limited success. One of the problems is that the drugs are not targeted, acting on many genes at once, not just those linked to cancer, which means they come with toxic side effects.
But epigenome editing can be made precise by harnessing the same enzymes cells use to turn their genes on and off. Researchers attach key components of these proteins to a gene-editing protein, such as a ‘dead’ version of CRISPR’s Cas9 protein, capable of heading to a specific location in the genome but unable to cut DNA . Their effects can vary: one editor may remove histone tags to turn on a gene, while another may add methyl groups to DNA to repress it.
Two decades ago, biotech company Sangamo Therapeutics designed an epigenome editor using this method that revealed a gene called VEGF, which helps promote blood vessel growth, in hopes of restoring blood flow in people with neuropathy due to diabetes. The company injected DNA coding for the editor into the leg muscles of about 70 patients in a clinical trial, but the treatment didn’t work very well. “We couldn’t deliver it efficiently” to muscle tissue, says Fyodor Urnov, a former Sangamo scientist now at the Institute for Innovative Genomics at the University of California (UC) Berkeley.
The company therefore turned to an adeno-associated virus (AAV), a harmless virus that has long been used in gene therapy to efficiently deliver DNA to cells. The cell’s protein-making machinery, it was thought, would use DNA coding for an epigenome editor as a regular supply. This strategy seems more promising: over the past 3 years, Sangamo has reported that in mice it can reduce brain levels of tau, a protein implicated in Alzheimer’s disease, as well as levels of the protein that causes Huntington’s disease.
Other teams working with mice are using the approach of delivering AAV to increase abnormally low levels of a protein to treat an inherited form of obesity, as well as Dravet syndrome, a severe form of obesity. epilepsy. Last year, a group used epigenome editing to turn off a gene involved in pain perception for months, a potential alternative to opioid drugs. Another team recently activated a gene with an epigenome editor delivered by a virus different from AAV. They injected it into young rats exposed to alcohol; the alcohol stifled the activity of a gene, which in turn left the animals anxious and prone to drinking. The epigenome editor woke up the gene and relieved symptoms, the team reported in May in Scientists progress.
Take control
In epigenome editing, a gene-editing tool such as a “dead” version of the Cas9 protein from CRISPR sits on top of a gene. Then, an attached “effector” protein adds or removes chemical tags on the DNA and histone proteins around which it wraps, increasing or decreasing gene activity.
The AAVs tested by many groups are expensive, and these DNA carriers, along with the foreign proteins they encode, can trigger an immune response. Another drawback is that the DNA loop encoding the epigenome editor is gradually lost in cells as they divide.
Last month, at the annual meeting of the American Society of Gene and Cell Therapy in Washington, DC, gene-editing experts proposed an alternative to avoid the drawbacks of AAVs. A key milestone for the group, led by Angelo Lombardo at the San Raffaele Telethon Institute for Gene Therapy, came in 2016, when he, Luigi Naldini and others reported in Cell that adding a cocktail of three different epigenome editors to cells in a Petri dish repressed gene expression and that this persisted as the cells divided.
This meant that instead of relying on AAVs to carry DNA from their epigenome editors – and force endless expression – they could use lipid nanoparticles, a kind of fat bubble, to carry its imprint in as messenger RNA (mRNA). This way, the cells only make the protein for a short time, which is less likely to trigger an immune response or change the epigenome in unwanted places. These nanoparticles are widely considered safe, especially after being injected into hundreds of millions of people over the past 2 years to deliver mRNA for COVID-19 vaccines.
It took several more years for the Italian team to convert their study in the laboratory into success in an animal. At the genomics meeting, postdoc Martino Cappelluti of Lombardo’s lab explained how the team injected mice with fat particles carrying mRNA-encoding epigenome editors designed to silence a live gene, PCSK9, which influences cholesterol levels. The strategy worked, with one injection suppressing blood levels of the PCSK9 protein by 50% and reducing low-density lipoprotein, or “bad,” cholesterol for at least 180 days.
“I see this as a tremendous breakthrough,” says Urnov, who hopes the lipid nanoparticle approach will soon be extended to other disease genes. “The key here is that you don’t need to have continuous expression of the epigenome editor,” says Jonathan Weissman of the Whitehead Institute. Work co-directed by Weissman reported last year in Cell on CRISPR-based enhanced epigenome editors that bring lasting change.
The researchers say epigenome editing could be particularly useful for controlling more than one gene, which is more difficult to do safely with DNA editing. This could treat conditions like Dravet syndrome where a person makes some of a needed protein but not enough, because like a dimmer switch, the strategy can modulate gene expression without turning it on or off completely. Several new companies hope to commercialize treatments using epigenome editors. (Gersbach and Urnov founded one, Tune Therapeutics; Lombardo, Naldini and Weissman are among the founders of another, Chroma Medicine.)
Despite the excitement, the researchers warn that it will take time for epigenome editing to have a broad impact. Editors don’t always work as advertised on some genes, says UC Davis epigenetics researcher David Segal. That may be partly because, as epigenetics researcher John Stamatoyannopoulos of the University of Washington, Seattle, worries, researchers don’t understand exactly what editors do once they infiltrate cells. . “It’s a black box,” he says.
Still, Stamatoyannopoulos agrees that epigenome editing has “tremendous promise.” Now researchers must refine their epigenome editors, try them on other diseased genes and tissues, and test them on larger animals for safety reasons before moving on to humans.