Comparative Genomics Identifies 3 Potential Therapies

Using a comparative genomics approach, researchers have identified three potential therapies for Rett syndrome that are being used or tested for other indications.

“This study highlights the potential of comparative genomics to accelerate drug discovery, and yields potential new avenues for the treatment of [Rett],” the researchers wrote. 

The study, “Expanding the MECP2 network using comparative genomics reveals potential therapeutic targets for Rett syndrome,” was published in the journal eLife. 

A hallmark of Rett syndrome is a deficiency in the MECP2 protein, which is known to activate or silence hundreds of genes that are critical in brain development and function. 

Although there are no disease-modifying therapies approved to treat Rett, research to restore the activity of the MECP2 gene that provides instructions for making the MECP2 protein is in the early preclinical stages, such as gene therapy which aims to produce a healthy gene. 

Another therapeutic strategy is to target proteins whose genes are affected by a MECP2 protein deficiency. To date, several ongoing clinical trials are evaluating potential therapies to modify the activity of these downstream proteins and reduce disease symptoms. 

Comparative genomics is a method that can be used to identify novel therapeutic targets altered by a lack of MECP2 via phylogenetic profiling (PP). That means finding genes and proteins connected to MECP2 across a related set of organisms, many of which use identical biological processes in nerve and brain development. 

This approach was investigated by researchers based in Israel and the United States, who combined a PP-derived map of proteins downstream of MECP2 and databases of medicines that have been validated to target specific proteins. 

“We combined our PP-derived interaction map of MECP2 with drug targeting databases to select new candidate drugs for [Rett],” the team wrote. 

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To generate a phylogenetic profile, computer searches were used to identify 390 genes from mammalian species, as well as eukaryotic species (organisms with a nucleus), that were highly correlated to interact with the MECP2 gene. 

The resulting profile was then cross-referenced to the DGIdb and Open Targets databases, which searched for specific medicines that affected these 390 gene candidates. From this, the team identified 33 proteins in the MECP2 phylogenetic network known to be targeted by medications. 

Of the 33 candidates, three MECP2-related proteins were found to be targeted by compounds with clinical efficacy and acceptable safety profiles. 

The first was the IRAK1 protein, which is blocked by pacritinib, an experimental therapy for two types of cancer. EPOR was the second, a receptor that binds EPO, a naturally produced hormone that stimulates the production of red blood cells and has neuroprotective effects. The third candidate protein was KEAP1, targeted by dimethyl fumarate (DMF) — marketed as Tecfidera, an approved treatment for multiple sclerosis and psoriasis.

The team then tested these potential therapies in four brain cell lines — microglial cells, astrocytes, primary neuronal cells, and neuronal stem cells (NSCs) — in which the MECP2 gene was silenced. In the first set of experiments, results showed that the applied doses of pacritinib, EPO, and DMF did not exert toxic effects on these four cells types.

Control and MECP2-silenced microglia, a type of immune cell in the brain, were treated with DMF, EPO, and pacritinib. EPO exerted the most significant effect, overriding the effects of MECP2 silencing in all five markers tested. In contrast, both DMF and pacritinib yielded only partial effects. Another experiment showed DMF treatment led to a significant increase in the immune activity of the silenced microglia cells, whereas EPO and pacritinib did not.

Silencing of MECP2 has been shown to increase the activity of the gene-controlling protein NF-kappaB, which has been associated with neuroinflammation in a Rett mouse model. Both EPO and DMF blocked NF-κB activation in MECP2-silenced microglia cells.

Studies suggest that astrocytes, a cell type that supports neurons in the brain, are implicated in Rett syndrome via neuroinflammation and other processes. The team found that MECP2-silencing increases the transition of neuronal stem cells into astrocytes at the expense of neurons. Treatment with pacritinib or DMF did not have significant effects on these processes. In contrast, EPO abrogated this impaired neuronal stem cell differentiation. Additionally, MECP2-silencing decreased the production of the transporter protein EAAT2. EPO blocked the decrease in EAAT2, but pacritinib and DMF did not.

Finally, one primary downstream gene target of MECP2 is brain-derived neurotrophic factor (BDNF), an essential regulator of neuronal development and function. In symptomatic mice that lack MECP2, BDNF levels are reduced. Here, silencing of MECP2 decreased BDNF production in both neurons and astrocytes.

Treatment with DMF and EPO increased BDNF gene activity in both silenced neurons and astrocytes, whereas pacritinib did not. A combination treatment of DMF and EPO in MECP2-silenced astrocytes showed a modest increase in BDNF, “suggesting potentially independent modes of action,” the researchers wrote. 

“In summary, EPO, DMF and pacritinib act differentially on MECP2-silenced NSCs, microglia and astrocytes, providing a preliminary validation of our approach,” the scientists wrote. “The investigation into specific drug effects and mechanisms of actions are important areas for future studies, as are drug combination assays and in-vivo studies of EPO, DMF and pacritinib using MECP2 [deficient] mice.”

“These will be to assess whether any of the identified drugs can be further be explored for clinical use,” they added.