Developing Epigenetic Drugs for Genetic and Regenerative Medicine

Tune Therapeutics cites animal studies showing that “genetic tuners” can change gene expression and preserve DNA sequences

Gene editing currently makes long-term changes to DNA sequences as a way of turning genes on or off. For many, however, the potential for permanent genetic changes is concerning. In contrast, a new approach known as “genetic tuning” manipulates the epigenetics of a cell and, in so doing, enables gene expression to be turned up or down.

“Genetic tuning can achieve a much greater dynamic range of effects … not turning a gene on or off, but turning it up or down a little,” Derek Jantz, PhD, chief scientific officer, Tune Therapeutics, tells GEN. “By tuning the epigenome, we can make precisely controlled changes to gene expression in much the same way that our cells do every day. Our cells don’t change their genome. Our cells change their epigenome.”

“We can also control the duration of the effect,” Jantz asserts. “We can make a change that will persist for days, weeks, or months.” He notes, however, that the optimal durations of such changes have not yet been determined.

“Basically, our epigenome editing platform, TEMPO, can change the way cells in the body interpret their underlying DNA sequence,” Jantz explains. “That allows us, potentially, to address some very common and very complex diseases that are caused by dysregulation of gene expression.”

First data, shared last May at the 26th Annual Meeting of the American Society of Gene and Cell Therapy (ASGCT), showed that in nonhuman primates, TEMPO downregulated the PCSK9 gene. The PCSK9 protein is important in regulating lipid homeostasis. “We now have a group of animals that have been treated and have significantly reduced cholesterol as a result,” Jantz says. “We can address cholesterol regulation directly—at the DNA level—without changing the underlying DNA sequence.” This approach could be significant for large indications that affect vast numbers of people.

How it works

“TEMPO is, basically, a toolkit that allows us to mix and match molecular parts in such a way as to achieve a particular manipulation of the epigenome of interest,” Jantz says. This toolkit has two sections. One consists of a DNA-binding domain, and the other incorporates one or more effector domains.

The DNA-binding domain is the protein Tune engineers use to target specific genes within the genome. The effector domains are attached to the DNA-binding domains and determine whether the gene of interest will be up- or downregulated. They also determine the strength of the effect and how long it will last.

Regulation largely focuses on DNA packaging—that is, on how tightly DNA is wrapped around packaging proteins called histones to form a dense, rope-like structure called chromatin. “Packaging DNA more tightly into chromatin is a good way of turning off the gene,” Jantz notes. “It basically blocks all of the other cellular machinery from reading the DNA.” Likewise, loosening the packaging improves access to DNA. Jantz holds that Tune can “go from closed and quiet to open and active.”

Another mechanism Tune leverages is DNA methylation. Adding or removing methyl groups changes the molecular structure of DNA slightly, affecting the binding of protein complexes that read and transcribe DNA into RNA. “The cell interprets the methylated DNA as a stop sign—something that tells it to ignore this particular instruction,” Jantz explains. “Removing DNA methylation from a gene tells the cell that the gene’s DNA instructions should be read.”

Tune Therapeutics employs epigenomic editing to tune gene expression up or down. Specifically, the company’s TEMPO platform alters DNA packaging—remodeling chromatin and modifying histones—without permanently altering the DNA itself. With the TEMPO platform, which incorporates a DNA-binding domain and one or more effector domains, gradated and reversible changes in gene expression are possible.

Impact on regenerative medicine

Jantz says that Tune is also exploring the long-term possibility of using TEMPO to enhance stem cells for regenerative medicine applications. The promise of stem cell therapy was that immature cells could be transformed into any other type of cell and implanted to restore cellular function. The reality, however, is that after a series of transformative manipulations, the result merely resembles the type of cell you wanted to make.

“It’s a bit of a cartoon character,” Jantz observes. “It has some of the properties of the cell you wanted to make, but it doesn’t necessarily behave exactly the same way because it’s not truly that type of cell.”

Stem cells are transformed into, for example, liver or muscle cells through epigenetics, via changes to DNA methylation and chromatin structure. “Our technology,” Jantz maintains, “is uniquely suited to fill the gap in stem cell therapies that we have today, in terms of transforming a stem cell to a cell that actually functions like the cell you’re trying to make.”

Expanding possibilities

Tune was formed in spring 2020 by three luminaries in the gene and cell therapy industry: Akira Matsuno, formerly of Juno Therapeutics; Charles Gershbach, PhD, director of the Duke Center for Advanced Genomic Technologies; and Fyodor Urnov, PhD, scientific director for technology and translation, Innovative Genomics Institute, University of California, Berkeley.

“At the time, DNA-binding domains were well established,” Jantz recalls. “What Charlie did was put the effector domains together with the DNA binding domains … thus creating tools we could direct to different locations in the genome.” Jantz adds that Gershbach subsequently developed a screening method to identify exactly where to put the TEMPO editor to achieve the desired outcome.

By December 2021, nearly two years later, New Enterprise Associates and Emerson Collective co-led a Series A funding of $40 million.

Until Tune did the work described in the company’s ASGCT announcement, data suggesting that long-term gene regulation was possible without changing the DNA sequence had been generated only in academic laboratories, usually in cultured cells in a Petri dish. In Tune’s ASGCT announcement, the company stated, “This data … represents the first demonstration of durable epigenetic gene regulation, in a large animal model, following transient delivery of an epi-editor.”

“The therapy is in the animal for only a few days,” Jantz relates. “It makes its changes to the DNA structure and the DNA methylation and then goes away, but the changes it made stay behind. Once we turn a gene off, it stays off. This is very exciting.”

Jantz says that before joining Tune at the beginning of the year, he would have said that the data set the company shared at ASGCT was impossible. Then he saw the data set and wanted to be a part of the company. “My entire career has been in gene editing, but what we’re doing here at Tune is unique,” he insists. “I think it will open people’s eyes to the potential of epigenetic control of gene expression.”

A sharp focus, myriad options

Right now, with its first programs still at the preclinical stage, Tune is bracing for the challenge of maintaining its focus while developing its pipeline. There is a wealth of potential applications across cell and gene therapy and regenerative medicine. Indeed, there is so much potential that Tune may be tempted to pursue too many applications. “The challenge for us,” he says, “has been identifying the best applications in terms of the areas of highest unmet needs among patients.” Tune’s goal, he continues, is to identify a few areas in which cell and gene therapies have been inadequate, but in which gene tuning could be highly effective.