During the height of the pandemic, Jennifer Kwon, PhD, became one of the first scientists hired by a new company focused on epigenome editing—Tune Therapeutics. She joined the company almost immediately after completing her PhD in the lab of Charles Gersbach, PhD, director of Duke University’s Center for Advanced Genomic Technologies and one of Tune’s co-founders. The other two co-founders are Akira Matsuno, president and CFO, and Fyodor Urnov, PhD, scientific director, technology and translation with the Innovative Genomics Institute.

There were a lot of Zoom meetings in Tune’s first few months, she said. But once they were able to grab a few benches during the summer of 2020, they moved quickly.

Jennifer Kwon, PhD

Now, just three years later, Kwon presented the company’s first data in a late-breaking presentation at the ASGCT meeting in Los Angeles. In doing so, she detailed the first successful example of epigenetic editing in non-human primates.

The company’s first target is PCSK9, a protein mainly responsible for regulating cholesterol in the bloodstream, and a common therapeutic target for the prevention of cardiovascular disease. Silencing PCSK9 results in a reduction of LDL cholesterol.

Tune’s presentation on Friday was titled “Transient Delivery of Epigenome Editors Stably Represses PCSK9 and Lowers LDL Cholesterol in Non-Human Primates.”

The researchers started testing their system of epigenetic repression in human liver cell lines. To do this, they developed an epigenome editor (epieditor) targeting the PCSK9 promoter and were able to show repression in the hepatoma cell line for six months. And because those cells are repeatedly dividing, the team concluded that the repression was heritable. They also confirmed the mechanism of action—deposition of methylation at CpG dinucleotides—in vitro.

After one dose of epieditor repressed PCSK9 in the cell line for six months, the team moved into primary hepatocytes. Again, they saw a large amount (93%) of PCSK9 mRNA repression.

Based on these data, they moved into a non-human primate, delivering a lipid nanoparticle (LNP) carrying RNA encoding an epi-repressor targeted to the PCSK9 promoter of cynomolgus macaques into three monkeys (with two saline-only control monkeys.) They saw a reduction in both serum PCSK9 and LDL-C—a 75% target repression out to four months, so far. Each week, the team performs blood draws to measure the LDL cholesterol readouts, and also perform ELISA assays on PCSK9 to measure the target protein readout.

The mechanism of action of the epi-repressor was confirmed by analyzing methylation signatures in liver biopsies. More specifically, the team wrote, “The region surrounding the gRNA target site was sequenced and differential CpG methylation was quantified. In animals treated with the epi-repressor, peak methylation occurred in the region surrounding the gRNA binding site, with up to 68% CpG methylation at certain residues compared to ~1% in PBS controls. We observed the spread of methylation was limited to a ~2.6kb region surrounding the PCSK9 CpG island.”

What are the advantages of epigenetic editing over typical CRISPR gene editing? Epigenome editing does not cut or nick the DNA, eliminating some of the risks such as chromosomal translocations. In addition, Kwon told GEN that epigenome editing could be applied to complex diseases where one gene may need to be up-regulated and another down-regulated at the same time. And, while currently approved PCSK9 treatments require repeat administration every few months, epigenetic editing could potentially allow for sustained repression without direct edits to the genome.

Why might the epiediting be longer lasting? Kwon said that most of the CpG dinucleotides in the genome are methylated at steady state and are heritable over time. She told GEN that by depositing the methyl marks, Tune is mimicking that natural biology. The sustainability of the methylation pattern, and the consistency between animals, she said, have been the most exciting results.

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