Epigenetic Editing Enters the Clinic: First Trial Data and a Pipeline Poised to Redefine Gene Therapy
Key Insights
Epigenetic editing precisely silences or activates genes without cutting DNA, avoiding risks of off-target mutations and chromosomal rearrangements inherent to gene editing.
Early-stage clinical trials are underway for FSHD muscular dystrophy and chronic hepatitis B (search), with one trial showing elimination of viral biomarkers for up to 17 months.
nChroma's PCSK9-targeting epigenetic editor reduced 'bad' cholesterol by approximately 70% in monkeys after a single injection, with effects lasting nearly a year in mice.
After two decades of battling scientific dogma, epigenetic editing has arrived in the clinic. At the International Research Congress on FSHD held in late June in Chicago, Epicrispr Biotechnologies (search) became one of the first companies to announce data from an epigenetic-editing trial, marking a pivotal moment for a field that promises to control gene expression without altering the underlying DNA sequence.
The approach stands in elegant contrast to conventional CRISPR gene editing. Rather than cutting DNA and relying on cellular repair machinery, epigenetic editors use a catalytically "dead" Cas enzyme — one that cannot slice genetic material — fused to effector proteins that add or remove chemical tags on DNA and histones. "Epigenetic editing is a truly exciting concept for therapeutics because there is no chance of off-target DNA mutations being made, as is the case with gene editing," explains Jessica Tyler, a molecular biologist at Weill Cornell Medicine in New York City.
A gentler approach to gene regulation
The basic epigenetic editor has two components: a targeting mechanism, generally a nuclease-deactivated CRISPR–Cas enzyme guided by RNA, and an effector that modifies epigenetic marks or recruits transcriptional machinery. Some effectors, such as methyltransferases and demethylases, directly modify DNA and histones. Others function as artificial transcription factors that recruit or block the cell's own gene-expression machinery.
"I find epigenome editing to be much more sophisticated, much more complex," says Charles Gersbach, a biomedical engineer at Duke University in Durham, North Carolina. "There are just so many more things that you can do with epigenome editing that aren't necessarily doable with genome editing."
Because epigenetic editing does not create double-stranded DNA breaks, researchers can target multiple genomic sites simultaneously by adding several guide RNAs — a feat that would risk dangerous chromosomal rearrangements with conventional gene editing.
From the laboratory to the liver
The translational momentum is building rapidly. In January 2025, nChroma Bio (search), based in Boston, Massachusetts, began dosing patients with chronic hepatitis B (search) using an experimental epigenetic silencer. The therapy aims to silence viral genomes — both those integrated into host chromosomes and those existing as extrachromosomal DNA — to prevent production of viral particles and achieve what researchers describe as a "functional cure."
At the European Association for the Study of the Liver conference in Barcelona in May, Tune Therapeutics (search), co-founded by Gersbach and based in Seattle, Washington, reported that in an ongoing early-stage trial, higher doses of its epigenetic treatment eliminated several viral protein and RNA biomarkers for up to 17 months.
Meanwhile, nChroma's PCSK9 programme has demonstrated striking preclinical results. In a study published in 2025, the company's epigenetic-editing system, encapsulated in lipid nanoparticles and delivered intravenously, silenced expression of a human PCSK9 transgene in mice, leading to a reduction of more than 98% in protein levels for at least a year. In cynomolgus monkeys, the same treatment slashed PCSK9 levels by about 90%, and levels of low-density lipoprotein cholesterol dropped by approximately 70%. Importantly, when researchers removed part of the liver in four mice, forcing the organ to regenerate, the new tissue maintained the epigenetic repression — demonstrating that the silencing can be passed from mother cell to daughter.
Hit-and-run silencing with lasting effects
Angelo Lombardo, a molecular biologist at the San Raffaele Hospitalization and Treatment Institute for Gene Therapy in Milan, Italy, described a method he calls "hit and run" editing in 2016. The system relies on the KRAB transcriptional repressor domain and a methyltransferase enzyme, along with customizable DNA-targeting molecules. Short-term expression of these constructs places repressive marks on target genes, shutting them off for months across several rounds of cell division.
Lombardo's team used this system to deactivate the Pcsk9 gene in mice. A single treatment delivered via lipid nanoparticles carrying messenger RNA encoding the epigenetic editor nearly halved PCSK9 levels, with effects lasting almost a year. Lombardo co-founded nChroma to advance such programmes.
FSHD and the personal mission
For Amber Salzman, chief executive of Epicrispr Biotechnologies (search), the pursuit of epigenetic editing is deeply personal. FSHD — facioscapulohumeral muscular dystrophy (search) — is an inherited disorder causing progressive muscle weakness that begins in the face and upper body. Salzman's husband had several relatives with the disease. "At the time, nobody really understood what caused it," Salzman recalled. When she interviewed with Epicrispr and learned the company was targeting FSHD, she took the job.
Epicrispr, based in South San Francisco, uses a compact Cas12F enzyme — roughly 500 amino acids compared to Cas9's approximately 1,300 — discovered in archaea. The smaller size allows the system to be packaged into adeno-associated virus vectors for delivery. Founder Stanley Qi, who worked in the lab of CRISPR pioneer Jennifer Doudna at the University of California, Berkeley, was among the first to repurpose Cas9 as a "dead" enzyme for epigenetic targeting in 2013.
A complex regulatory landscape
Despite the promise, the epigenome's complexity presents formidable challenges. Human gene expression is managed by about 900 chromatin regulators and 1,600 transcription factors. "We really don't understand the rules," says Marianne Rots, an epigeneticist at the University Medical Center Groningen in the Netherlands. "We cannot predict the final outcome of our biological experiments."
Bioethicist Yann Joly, who heads McGill University's Centre of Genomics and Policy in Montreal, urges caution: "Epigenetic regulation plays a central role in development and reproduction." The community must ensure therapies are delivered safely and without unintended consequences.
Yet the flexibility of the platform continues to attract innovation. Lombardo's group recently combined epigenetic editing with gene editing in an all-in-one platform for CAR-T cancer therapy, using full-length guide RNAs to direct genetic insertion of the CAR while truncated guide RNAs recruit epigenetic silencers to other genes — achieving both modifications in 80% of cells in culture.
More than a dozen companies are now exploring epigenetic-editing technology. As trials progress and mechanistic understanding deepens, the field is poised to deliver therapies that are tunable, reversible, and — crucially — gentler on the genome.