Back in 1942, the term epigenetics was introduced by Conrad Waddington to present a picture of cell development, one in which cells descended a hillside and followed diverging valley paths before settling into different cellular identities. Subsequently, as the physical nature of genes and gene expression became clearer, the meaning of epigenetics became more technical. It also acquired, in addition to its original descriptive sense, a prescriptive sense. That is, epigenetics came to encompass the development of epigenetic interventions.
Today, no account of epigenetics is complete if it doesn’t describe how epigenetic mechanisms are being exploited to develop epigenetics-based technologies that promise to transform research and clinical medicine. Among the growing number of distinct epigenetic changes being uncovered, DNA methylation and histone acetylation and methylation are among the best understood, and they are being assessed at ever-higher resolutions and throughputs. Such advances are now paving the way toward applications that just years ago seemed unattainable, such as analyzing DNA methylation patterns during surgeries to classify and manage malignancies, epigenetically manipulating adipose cells to treat obesity, and reversing disease-related cellular aging.
Nanopore technology for DNA and RNA methylation analysis
“Our way to call DNA methylation is very robust and accurate, and we have seen several instances where we are the most reliable platform to do this,” says Sissel Juul, PhD, vice president, applications, Oxford Nanopore Technologies (ONT). Supporting her claim, the first systematic comparison of CpG methylation detection tools using long-read sequencing methods, published in March 2024, examined over 7,000 nanopore-sequenced samples from various studies at deCODE Genetics and revealed that ONT’s nanopore technology performs comparably to or better than other sequencing and data analysis platforms currently available.
ONT scientists have developed various nanopore-based approaches to interrogate various types of epigenetic changes in DNA and RNA. For example, MinION, the first commercial sequencer using nanopore technology and launched by ONT in 2014, has the ability to discriminate cytosine from all four known types of epigenetic modifications that can be present on this base.
One of the current challenges in the field is that, besides the epigenetic changes in DNA, over 160 distinct types of covalent changes were reported in RNA, but most of them have been insufficiently characterized in terms of their abundance and biological relevance. “When it comes to RNA, we have the only platform capable of detecting modifications directly,” Juul asserts. “But it is unclear, for example, how important a traditional 5-mC is on RNA compared to all the other modifications.”
Except for a few types of epigenetic modifications, the analysis of most types of epigenetic changes is still limited to research applications and is not performed broadly in the clinical setting. “It is not that they are not important,” Juul notes, “it’s just that we simply don’t know how important they are.”
Moreover, because all the methods that have examined the various types of epigenetic modifications are indirect in some way, the rapid and high-throughput screening using the ONT platforms presents another conundrum. “Our biggest challenge is not just being able to detect the various modifications, but making sense of what we see when we don’t yet know what we are looking for,” Juul says.
DNA methylation analysis during surgery for cancer classification
Using extensive computational resources, scientists led by Jeroen de Ridder, PhD, associate professor in the Center for Molecular Medicine of the UMC Utrecht and a principal investigator at the Oncode Institute, developed Sturgeon, a patient-agnostic transfer-learned neural network classifier. It allows central nervous system malignancies to be subclassified based on sparse DNA methylation profiles obtained with rapid ONT sequencing during brain surgery.
In a study on pediatric and adult surgeries, Sturgeon provided an accurate diagnosis within 40 minutes for 90% of the cancer samples. “We want to see that the proof of concept we just achieved will be applied at a much broader scale in the future,” de Ridder says. “We have substantial evidence to support the ability of this approach to make a difference for patients.”
A unique challenge in the case of brain cancer is that performing biopsies is usually possible only during surgery, which is also the first time when the medical team can learn about the pathology. However, historically, biopsy results for most cancers generally become available only after one to two weeks.
“That waiting time increases distress, anxiety, and psychological burden in the patient,” de Ridder points out. Shortening the waiting time by providing biopsy results the same or next day would support a much more rapid response by the healthcare team.
DNA methylation–based cancer classification during surgery may have yet another advantage. “If the brain tumor type is known during surgery, there might be an opportunity to start treatment by locally delivering the right therapeutic agent,” de Ridder says. The Sturgeon proof of concept suggests that cancers could be evaluated at other locations as well, expediting treatments and even reshaping patient care in oncology.
Epigenomic controllers delivered into cells
“We harness the power of epigenetics by using mRNA therapeutics as programmable epigenomic medicines,” says Mahesh Karande, president and CEO, Omega Therapeutics. The approach at Omega takes advantage of the organization of genes and regulatory elements into conserved three-dimensional chromatin loops, a structural feature that is also highly conserved across species.
“There are about 15,000 of these loops, which we call ‘insulated genomic domains,’ and each of them contains single or multiple genes together with their regulatory elements,” Karande notes. The regulatory elements, he continues, have unique genomic sequences, which makes them attractive therapeutic targets. He adds, “We have mapped the regulatory elements of these insulated genomic domains and created our database of targets, which we call EpiZips.” These EpiZips, or epigenomic ZIP codes, can be targeted by programmable, modular mRNA-based epigenomic drugs, known as Epigenomic Controllers, each of which provides a unique opportunity for further drug development.
Epigenomic Controllers, delivered into cells using lipid nanoparticle technologies, are translated on the ribosomes into the respective therapeutic proteins. The fusion proteins contain a highly specific, proprietary DNA-binding domain, which is connected through a linker to an epigenomic effector domain that controls gene expression regulators at target insulated genomic domains. “Omega’s mRNA therapeutics lay an epigenomic mark, which is chosen from a vast repertoire of mammalian epigenomic effectors that are available for us and for which we have a library across cell types,” Karande explains.
The assets in the Omega pipeline are available to several of the company’s discovery programs including those for oncology, monogenic and multigenic conditions, and regenerative medicine. A recent collaboration between Omega and Novo Nordisk leverages Epigenomic Controllers to enhance metabolic activity, as a part of a novel therapeutic approach for obesity management. “We are working to transdifferentiate white fat into brown fat,” Karande says. “We think that this approach could potentially be curative.”
Epigenetically reversing age-related diseases
“With an increasing understanding that aging is not necessarily just normal wear and tear, but that it involves a distinct set of biological changes, we are focusing on treating aging-related diseases,” says Sharon Rosenzweig-Lipson, PhD, the CSO of Life Biosciences. One of the company’s main approaches is to meet this therapeutic need by inducing cellular rejuvenation through partial epigenetic reprogramming.
“Starting with a mature injured cell, we can turn back the clock to convert that cell to a more youthful state but, importantly, without going all the way back to a stem cell,” Rosenzweig-Lipson asserts. Following the discovery by Shinya Yamanaka, MD, PhD, and his colleagues that four transcription factors (Oct4, Sox2, Klf4, and c-Myc) together can convert a mature cell into an induced pluripotent stem cell, an important advancement was that c-Myc, an oncogene that can have teratogenic effects, is dispensable for this process. Another advancement concerns the remaining three transcription factors, which together are known as OSK. “The partial epigenetic reprogramming approach with OSK reprograms the cell to a more youthful state but maintains the cell’s identity,” Rosenzweig-Lipson points out. “That’s an important distinction of our program.”
Aging is accompanied by the accumulation of epigenetic changes, such as DNA hypermethylation at promoters, and OSK can remove that aberrant methylation. “And data show that reducing hypermethylation restores cells to a more youthful state,” Rosenzweig-
Lipson reports.
A lead asset in the Life Biosciences pipeline, ER-100, enables expression of Oct4, Sox2, and Klf4 upon doxycycline administration, and in mouse models of glaucoma, it showed beneficial effects that included improvements in visual function, axonal regeneration, and increased survival of retinal ganglion cells.
“Last year, we translated this approach from mice to nonhuman primates,” Rosenzweig-Lipson says. Scientists at Life Biosciences utilized a laser-induced model of nonarteritic anterior ischemic optic neuropathy, an age-related condition that is the most common acute neuropathy after age 50 and for which no effective current treatments exist.
“We demonstrated that ER-100 improved retinal electroretinogram patterns and led to improvements in axon density,” Rosenzweig-Lipson relates. These benefits were seen even when treatment was initiated one day after injury. “Optic neuropathies are just the beginning,” she declares. “But there are so many opportunities because a host of age-related diseases could benefit from this approach.”
