In addition to characterizing the genetic basis for different cancers, scientists are increasingly interested in the role of the epigenome in tumor development, and possible therapies that can target genes repressed by chemically modifying chromatin in cancer. 

Part of what makes the epigenome an attractive target is the possibility of hitting a system of proteins involved in gene expression programming rather than a single target, according to Karmella Haynes, PhD, an assistant professor of biomedical engineering at Emory University. She and a team of scientists from Emory University and Georgia Institute of Technology have developed another potential approach for reactivating repressed tumor suppressor genes that could ultimately have implications for how solid tumors like triple-negative breast cancer (TNBC) are treated. 

Their method uses engineered proteins called synthetic reader-actuators (SRAs) which are designed to reactivate epigenetically-silenced gene expression. Haynes’ team is the first to study the use of these kinds of engineered proteins for epigenetic cancer therapies and specifically in TNBC cases. Full details of their work are published in the most recent issue of GEN Biotechnology in a paper titled “Synthetic Reader-Actuators Targeted to Polycomb-Silenced Genes Block Triple-Negative Breast Cancer Proliferation and Invasion.” 

Cancer cells have multiple mechanisms in place that help them resist treatment and sustain growth even when targeted by powerful therapies. In TNBC cases for example, “nearly 80% of TNBC patients who receive neoadjuvant chemotherapy experience recurrence and metastases to the brain and lungs, which occur more often and are deadlier than for other types of breast cancer,” the researchers wrote in the paper. For this reason, “a narrow single targeting approach does not always work. You are not addressing mechanisms that act as a backup,” Haynes, who is the senior author on the paper, explained to GEN

An important feature of TNBC is the heterogeneity of the tumor cells which is tied to differences in which genes are expressed in each specific cell. This makes it a good candidate for an epigenetic-based therapy that targets silenced genes for reactivation. Also, with an epigenetic approach, “you can potentially affect the expression of multiple genes so you have a stronger effect on the cancer,” Haynes said. “This broader multi-gene approach is more robust in principle. You are more likely to successfully affect more cells.”

Some attempts at epigenetic cancer therapy use compounds that target and inhibit polycomb proteins—epigenetic regulators of transcription in cells. However, these approaches have had poor results in clinical trials involving solid tumors possibly because many of the transcription-activating proteins that these drugs target are often mutated in these cases. 

So far, the FDA has approved a single epigenetic-based treatment, tazemetostat, which inhibits a polycomb protein called EZH2. The drug is approved for adult patients with relapsed or refractory follicular lymphoma who have a positive EZH2 mutation and have received two previous systemic therapies. The drug, which was approved in 2020, is marketed under the brand name Tazverik. 

Haynes and her team used a different approach. For their study, they used an SRA designed to bind a trimethylated histone in polycomb chromatin. According to the paper, SRAs recruit transcription factors that bind to polycomb chromatin sites and reactivate the expression of important tumor suppressor genes. When they used their SRA to treat in vitro models of TNBC, the results were very promising. The data from the models showed that the cancer cells’ growth slowed, tumors were less invasive, and there were greater levels of apoptosis observed. 

This paper builds on earlier published work, including this one, from Haynes and her colleagues that explored how SRAs interact with their targets. The GEN Biotech study is the first paper “where we show that the epigenetic targeting approach has some consequences in how cells respond. We are actually showing some outcomes,” Haynes said. “We were able to connect [the SRA] with chances in gene expression programming at the same time as seeing the cells lose their ability to invade and a decrease in the size of the tumor.”

This study was done in in vitro models, which are a long way from human trials but these early results are promising. Some next steps would be additional testing in cellular models followed possibly by testing in mice. Among other experiments, Haynes said that she would be interested in studying the impact of SRAs on tumor development in hypoxic mouse models—there is some evidence reported in the paper that indicates that it works in hypoxic TNBC cells in vivo. Additionally, she also wants to test possible effects of SRAs when they are exposed to normal cells. 

Further down the road, Haynes and her team could also compare the performance of their protein to the FDA-approved tazemetostat. Some results from testing tazemetostat on TNBC that are reported in the paper suggest that it “only reduces TNBC cell viability by 50% even at high concentrations.” For the current study, the scientists compared their engineered protein to other small molecule epigenetic drugs. With those drugs, the change in gene expression programming in response treatment was not as clear cut. That same connection to gene expression is much clearer with the engineered protein because it is designed from the ground up to have a specific protein-protein interaction. 

Furthermore, before SRAs can be used as therapeutics, Haynes and her team would need to figure out an appropriate delivery mechanism. “We would have to show that we can deliver the protein and modify it to make it sticky on cancer,” she said.  She hopes they will be able to test various mechanisms for delivering the protein including direct uptake or possibly using adeno-associated viral vectors, which are currently used in gene editing.  

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