Tag: Epigenomics

When John McHutchison, MD, the former head of research and development at Gilead and a leading figure in hepatitis virus therapeutics, saw Tune Therapeutics’ preclinical data on sustained epigenetic silencing of the hepatitis B virus (HBV), he knew it was time for a major pivot.

“When I saw the Tune data on the long-term silencing of an infected cell line for 500 days, I realized it had never been seen before,” McHutchison told Inside Precision Medicine. “I was at Gilead for ten years, where I was head of research and development and worked on all the other viruses, including hepatitis C (HCV)… We spent a decade at Gilead trying to silence this mechanism without success.”

McHutchinson decided to get plugged into Tune Therapeutics, which was founded by Akira Matsuno, Charles Gersbach, PhD, and Fyodor Urnov, PhD, to develop epigenetic therapies that precisely control gene expression without altering DNA sequences. In January 2023, McHutchinson joined Tune’s board of directors and, two years later, became CEO and chairman in March 2025. That preclinical silencing has now shown promise in translating to the clinical setting.

Last month at the European Association for the Study of Liver (EASL) Congress in Barcelona, Spain, Tune presented the first clinical evidence of epigenetic silencing in HBV. The Phase Ia/IIb clinical data shows deep and durable antiviral activity, including silencing of both the integrated virus and covalently closed circular DNA (cccDNA)—a stable viral mini-chromosome that resides inside liver cell nuclei and continually produces new virus particles—offering a possible pathway to a lasting therapeutic effect for HBV patients.

“Now we have the data that shows we can durably silence a gene of interest in humans by modulating epigenetics without cutting,” McHutchison said. “That’s a big deal. The de-risking of the technology.”

Swimming upstream

More than 240 million people worldwide live with chronic HBV infection. Current antiviral therapies can suppress viral replication for years, sometimes decades, but they rarely eliminate the virus entirely. Once treatment stops, viral replication almost always returns. The central problem is cccDNA, often referred to as HBV’s “molecular reservoir,” which acts as a stubborn, self-renewing blueprint, making chronic HBV highly difficult to eradicate or cure.

“It’s also not lost on me that for a decade, our industry has poured billions of dollars into HBV, but without success,” said McHutchinson. “Why is that? Why didn’t we get there? Because we weren’t transcriptionally silencing the reservoir. We were working downstream.”

McHutchinson points out that even the most recent genetic medicines that have shown promise, such as the experimental HBV drug, an antisense oligonucleotide (ASO) called bepirovirsen developed by GSK, still work downstream. Bepirovirsen does not eliminate HBV’s reservoir of cccDNA inside liver cells. Instead, it targets and destroys HBV RNA transcripts, reducing viral replication and lowering the production of viral proteins such as HBsAg, while also helping restore immune responses against infected cells. Because the drug leaves cccDNA intact, its goal is not a cure at the genetic level but instead a functional one, where the immune system keeps the virus permanently suppressed or undetectable after treatment ends.

“You’d silence reverse transcription or cut it with siRNA, and things would fall in the serum, but you wouldn’t affect the reservoir,” said McHutchinson. “As soon as those drugs were removed, the reservoir started to make new viruses again. Nobody is, in essence, being cured. But here we’re working upstream, where the progeny and the new virus are being made.”

GSK may not see eye to eye with McHutchinson on bepirovirsen, which, according to a recent press release, “achieved functional cures in 19% of participants in two large Phase III trials when added to standard antiviral treatment for six months.” Chronic hepatitis B (CHB) is considered “functionally cured” when the blood has no detectable hepatitis B surface antigen or virus DNA for at least 24 weeks after a finite treatment course, allowing immune control without medication and reducing the risk of liver complications, including liver cancer, and all-cause mortality.

However, to McHutchinson, a functional cure and a genetic cure are apples and oranges. “That’s just stimulating an innate immunity,” he said. “It’s an injection a week for 24 weeks, and it’s an ISO that stimulates innate immunity—that’s why it’s curing one in five people who have low levels of HBV surface antigens. It’s a positive development for the field that something else could be approved. I speak admirably about that. But it’s not a panacea. And there’s a lot of room for many other people to come along with better things and better combinations.”

Durable biomarker suppression

Tune’s ongoing Phase Ib/IIa trial includes four dose levels of its therapy, administered as a single intravenous infusion, in 19 people. The dose cohorts ranged from 0.2 mg/kg to 0.85 mg/kg, as well as a multiple-dose cohort receiving up to three infusions. Another seven people got up to three infusions of the second-highest dose given at least four weeks apart, for a total of 26 participants, which McHutchinson acknowledged is quite small.

According to Tune, antiviral activity was seen across all major HBV biomarkers, including surface antigen (HBsAg), pregenomic RNA (pgRNA), e-antigen (HBeAg), HB core-related antigen (HBcrAg), and phosphorylated HBV core antigen. Tune reported that biomarker repression occurred in 100% of participants treated at dose levels two through four. Particularly striking were signs suggesting direct cccDNA silencing. Among HBeAg-negative patients treated at higher dose levels, four of seven lost detectable pgRNA, while three of those patients also lost HBcrAg. In HBeAg-positive patients, three of five lost detectable HBeAg.

McHutchison emphasized that the most encouraging signal may be durability. “Some of those patient graphs we showed have durability up to 250 or 300 days,” he said. “These genes have plateaued at very low levels and haven’t come back with a single application, which suggests and proves what we thought preclinically—that the methylation fingerprint and chromatin compaction are durable and don’t seem to leak or relapse.”

According to the company, suppression following a single dose has now been observed for as long as 17 months in some patients. As with any first-in-class therapy, safety remains a major focus. So far, Tune says TUNE-401 has shown a “favorable safety profile,” with mild to moderate infusion-related reactions, transient liver enzyme elevations, and temporary platelet reductions that resolved without major complications. “We have an acceptable and good safety profile compared to others,” McHutchison said. “What we are seeing in terms of AST and ALT elevations, infusion-related reactions, and transient reductions in platelets are pretty much in line with or better than what others are seeing with similar LNP products.”

Importantly, the company says it has not yet observed additive toxicity in patients receiving multiple doses. Whether multiple doses will ultimately be necessary remains uncertain. “There are examples in the presentation of a profound effect with a single dose and another patient who showed benefit from a second dose,” McHutchison said. “That’s still to be determined.”

Tune plans to continue dose optimization in Phase II, including testing additional multidose regimens and potentially escalating to even higher doses. “We’re tinkering with the maximum dose, trying to optimize it while keeping safety in mind,” he said.

Diversity, in patient and virus

The technology underlying TUNE-401 sits at the intersection of gene therapy, RNA therapeutics, and epigenetics. Rather than editing DNA permanently, the therapy uses a methyltransferase enzyme and the KRAB domain chromatin-compacting protein module to alter the epigenetic state surrounding HBV DNA.

“Once you’ve laid down that pattern, it is permanent and inheritable through cell division,” McHutchison explained. “We can vary the degree of silencing with our platform: 30%, 50%, 80%, or 100%. For hepatitis B, we tried for complete suppression.”

The concept of epigenetically programming cells has attracted growing interest across biotechnology, particularly as concerns remain about irreversible DNA editing approaches. “We feel, because we’re not editing, we can go after common diseases,” McHutchison said. “We’re looking at cardiovascular targets and a diabetes program as well. That’s what the technology can do without editing. But you have to get it there potently and safely.”

One of the key questions moving forward is whether the therapy will work consistently across the enormous genetic diversity of HBV strains worldwide. The current study spans sites in New Zealand, Hong Kong, and Moldova, intentionally capturing ethnically and geographically diverse patient populations. “There is viral diversity across various geographical areas, probably due to evolution and migration patterns over thousands of years,” McHutchison said. “We’ll be able to look at responses according to genotype.”

Tune estimates its targeting system covers approximately 98.5% of known HBV sequence variants based on historical databases. However, the company acknowledges that some patients in lower-dose groups showed weaker responses, raising questions about viral sequence variability. “We’ll be looking at whether there was a mutation or sequence difference from our target,” McHutchison said. Those analyses are expected later this year as additional viral sequencing data becomes available.

Addressing the applicability of TUNE-401 in diverse populations of people and viruses depends on something that Tune hasn’t yet got—numbers. That’s where GSK’s bepirovirsen holds a massive edge, with the two Phase III efficacy trials having involved more than 1,800 participants in 29 countries. The trial for TUNE-401 reported data from about 1–2% of GSK’s entire cohort.

A potential turning point

For McHutchison, the development path may resemble the evolution of HCV treatment, where he played a central role during his years at Gilead. He points to Pharmasset and the development of sofosbuvir (Sovaldi), a direct-acting nucleotide analog that blocks the virus’s essential protein (NS5B polymerase), which became the backbone of curative HCV regimens. “People forget that Sovaldi didn’t work that well by itself initially,” McHutchison said. “It had to be combined with ribavirin and interferon. But it was the backbone mechanism. I think in essence we have that backbone mechanism here.”

TUNE-401 could serve as the foundation for combination regimens capable of delivering a total remission from HBV. The company plans to initiate a larger Phase II study as early as late 2026, exploring combinations alongside optimized dosing schedules. “The approval endpoint for a finite HBV therapy is to drive these biomarkers negative, remove background therapy, and make sure people don’t relapse,” McHutchison said.

Many hurdles remain before TUNE-401 could approach regulatory approval. The current data comes from a small early-stage trial, long-term durability remains unproven, and the field has seen many HBV programs falter after initially promising signals. Still, the idea of directly silencing cccDNA—rather than merely suppressing downstream viral activity—represents a conceptual shift that many hepatologists have sought for decades.

“Over the prior 30 years in hepatology, I have rarely seen a clinical signal this clear,” McHutchison said.

The company’s broader ambitions extend beyond infectious disease. Tune has previously disclosed programs in cardiovascular disease and type 1 diabetes, where epigenetic modulation could potentially alter cellular function without permanent genomic changes. Still, HBV offers perhaps the clearest proving ground for the platform because the virus depends so heavily on transcriptional activity from cccDNA.

Whether Tune’s epigenetic editing approach succeeds remains uncertain. But for a field long defined by incremental advances and repeated disappointments, the data presented in Barcelona may represent something increasingly rare in HBV research: a plausible new path towards a cure.

And for McHutchison, it closes a loop that began years earlier in Gilead’s hepatitis research labs. “We knew this mechanism mattered,” he said. “The technology just didn’t exist yet. Now it does.”

The post Phase Ib/IIa for Hepatitis B Epigenetic Silencer Shows Best-in-Class Potential appeared first on Inside Precision Medicine.

Researchers headed by a team at Icahn School of Medicine at Mount Sinai have discovered that many gut bacteria use a flexible survival strategy—known as epigenetic “bet-hedging”—to withstand disruptions such as antibiotics and diet changes.

Studying infant and gut microbiomes, the investigators showed that microbes can switch between functional states, rather than relying solely on genetic mutations, to try to survive shifting conditions. While bet-hedging has been observed in disease-causing bacteria, this is the first study to show that it is widespread among the beneficial microbes that make up the healthy human gut.

The findings shed light on a previously hidden layer of microbiome biology and may help explain why probiotics and fecal microbiota transplantation (FMT) produce inconsistent benefits across individuals.

Gang Fang, PhD, professor of genetics and genomic sciences and director of the Center for Genomic AI and Microbiome Medicine at the Icahn School of Medicine at Mount Sinai, is senior and corresponding author of the team’s published paper in Cell Host & Microbe, titled “Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.”

The human gut microbiome is constantly being disturbed—by medications, illness, and shifts in diet. Yet it often rebounds, the investigators noted. “In response to these alterations, the gut microbiome shows a remarkable adaptive capacity,” they wrote. “Characterizing this adaptive capacity is crucial for understanding the dynamic relationship between the gut microbiome and host physiology, especially in the context of human health and disease.”

Until now, scientists largely attributed this resilience to genetic mutations that accumulate over time.  But, as the authors continued, “Another mechanism of bacterial adaptation involves DNA methylation, which can regulate gene expression, enhance clonal heterogeneity, and mediate epigenetic phase variation (ePV, intra-strain epigenetic variation that leads to phenotypic differences … ePVs have been characterized in human pathogens, but their roles in commensals remain unclear.”

Fang continued, “Our study shows that there is another mechanism at work. Even within a single group of genetically identical bacteria, a small subset of cells exists in a different epigenetic state—where chemical tags on the DNA change how genes are turned on or off without altering the genetic code itself. That means some cells are essentially preprogrammed to respond differently to stress, giving the population a built-in survival advantage when conditions suddenly change.”

So when a stressor such as an antibiotic is introduced, this small subgroup can quickly become dominant because it is already primed to survive. When conditions change again, the population can shift back. This reversible strategy, known as “bet-hedging,” allows microbial communities to adapt rapidly to uncertainty.

To carry out their work, the researchers combined advanced DNA sequencing, large-scale data analysis, and laboratory experiments. They used long-read sequencing technology to analyze stool samples from infants before and after antibiotic treatment, as well as from FMT donor-recipient pairs. This approach allowed them to detect both genetic structure and epigenetic modifications simultaneously.

The scientists then analyzed more than 2,300 microbiome samples from previously published studies to determine how common this phenomenon is across individuals and bacterial species. To understand the mechanism in detail, the team isolated a beneficial gut bacterium, Akkermansia muciniphila, and tracked how its epigenetic states shifted in response to different antibiotics—identifying a specific gene involved in the process.

“Focusing on an Akkermansia muciniphila isolate, we find a specific ePV regulating mucC, a gene of unknown function but whose heterologous expression enhances bacterial tolerance to antibiotics via a bet-hedging strategy,” they stated. “Our results indicate that in the human gut, ePVs may help bacterial populations regain heterogeneity after bottlenecks encountered during colonization of a new host or severe perturbations due to antibiotic exposures.”

“Our work is the first to systematically demonstrate epigenetic bet-hedging across the human gut microbiome,” Fang noted. “It also identifies a specific gene that controls this switch in a beneficial bacterium and shows that the process is reversible—shifting in different directions depending on the type of antibiotic exposure. We were struck by how quickly small subpopulations could take over. In some cases, bacteria representing less than one percent of a population became dominant under changing conditions.”

The research team also found significant diversity within what had been considered a single bacterial strain. Even closely related cells could behave differently, with distinct gene activity and stress responses—highlighting how much remains to be understood about the microbiome at a deeper level. The findings help explain why the microbiome is resilient yet difficult to predict, and why microbiome-based treatments can produce variable results.

“At the same time, our study does not suggest that people should avoid antibiotics when they are medically necessary, nor does it recommend for or against any specific probiotic. Our research is aimed at understanding fundamental biology, not changing current medical care,” added Fang.

“Compared with genetic phase variation, ePV offers several advantages in enhancing clonal heterogeneity,” the team noted. “The reversibility of ePV, without altering DNA sequence or incurring mutation costs, serves as an additional way for individual bacterial strains to adapt to diverse stresses … Our results indicate that in the human gut, ePVs may help bacterial populations regain heterogeneity after bottlenecks encountered during colonization of a new host or severe perturbations  due to antibiotic exposures.”

The discoveries have several important implications for human health. In the field of probiotics, it may be that bacteria in a probiotic capsule are not in the same functional state as those that successfully establish themselves in the gut—potentially explaining inconsistent results. “Ultimately, our goal is to design probiotics that are better equipped to establish themselves in the gut and to develop therapies that support beneficial microbes while limiting harmful ones,” Fang said.

For FMT-based treatments, differences in these epigenetic states between donors and recipients may influence how well microbiota transplants work. And when considering antibiotic recovery, some gut bacteria may survive antibiotic treatment not because they are genetically resistant, but because a subset of cells is already in a protective epigenetic state that allows rapid rebound after treatment ends.

The research team plans to study larger groups of patients over time, particularly during and after antibiotic treatment and FMT. They also aim to explore whether similar mechanisms exist in other gut bacteria and to investigate how these epigenetic switches might be harnessed. In the longer term, understanding and potentially controlling these reversible switches could lead to more effective microbiome-based therapies, the investigators suggest.

“These ePV-driven regulatory mechanisms open new opportunities for targeted epigenetic interventions to improve the desired functions of beneficial bacteria,” the scientists stated. “For example, by manipulating ePV, we may strategically boost the resilience and functional capabilities of beneficial bacteria, which might improve the success rates of probiotic engraftment and the efficacy of treatments for microbiota-associated conditions.”

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