The biotech market is still going strong as more startups focused on therapeutic research crop up. Just this week, Italian startup Aptadir Therapeutics launched with $1.6 million to bring a new class of investigational drugs to the clinic.
The Milan-based startup is focused on correcting a chemical process known as DNA methylation to treat diseases that arise from its malfunction. DNA methylation occurs when methyl groups attach to DNA, influencing how genes work. However, when this process goes into overdrive — referred to as hypermethylation — it can lead to diseases like cancer and certain genetic disorders.
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Aberrant DNA methylation: cause for concern
Giovanni Amabile, executive chairman of Aptadir, explained that in cancer, key genes known as onco-suppressors, which normally prevent cancer cells from growing and dividing, become hypermethylated. This turns off their function, and therefore, allows cancer cells to proliferate.
“Basically, the blasts (immature cells) are not able to become monocytes or dendritic cells and they start to proliferate without differentiating into the right cell type,” said Amabile.
Hypermethylation is also a concern in genetic conditions like Fragile X syndrome (FXS), a neurodevelopmental disorder that affects around one in 11,000 people assigned female at birth and one in 7,000 people assigned male at birth, according to Cleveland Clinic. The condition is caused by hypermethylation in the FMR1 gene.
So, targeting this hypermethylation would be ideal. Aptadir has spotted RNA molecules that “basically act as a shield” and protect the genes from this dangerous methylation. These RNAs belong to a class called non-coding RNA, which doesn’t code for proteins. Scientists at Aptadir transformed these RNA molecules into a drug that takes the shape of an aptamer – single-stranded molecules that bind to targets.
“In order to make this suitable for clinical development, we transform it, the non-coding RNA, into an aptamer that has secondary and tertiary structures that make it very robust and resistant to degradation,” said Amabile.
Targeting cancer and Fragile X syndrome: two birds, one stone
Once the RNA drug enters the cells, it goes to the gene to prevent methylation and curbs any interaction with the enzyme responsible for the methylation process – DNA methyltransferase (DNMT).
“The DNMT1 is basically blocked from arrival on that gene,” said Amabile. “And we demonstrated that not only can we protect from additional methylation, but also progressively, the gene gets reactivated. In the case of cancer cell lines, we demonstrated that there is a progressive cell death of the cancer cells, and in the case of the X fragile cells, there is the reactivation of the gene that is exactly the pathogenetic event in this pediatric condition.”
The first of its kind, Aptadir’s technology is backed by data that was published in Nature more than a decade ago. A study titled ‘DNMT1-interacting RNAs block gene-specific DNA methylation’ was a turning point in therapeutic research. This was because it was never thought until then that RNAs could attach to DNMT1 proteins, since, as its name suggests, DNMT1 is meant to bind to DNA.
“I know that it is a bit surprising but these RNAs have a high affinity for DNMT1,” explained Amabile. “It was a big surprise because DNA-binding proteins are supposed to bind only to the DNA. And so, it was a big discovery to find that RNA has an even higher affinity than DNA with these RNAs. So, by inhibiting the catalysis site on the enzyme, it basically blocks the adding of the methyl group to the DNA.”
Touted as a “revolutionary finding,” the startup is now working on treating FXS and myelodysplastic syndrome (MDS), a blood cancer that affects the bone marrow and blood cells. Both in preclinical trials, the investigational cancer drug dubbed Ce-49, is being tested in patient samples as well as in animal models. However, these animal models are of chronic myeloid leukemia, another, more aggressive type of blood cancer. This is because models of MDS do not exist, Amabile pointed out.
“The literature has demonstrated that if you are able to achieve an efficacy response in this model, this can also be translated to the MDS model,” said Amabile.
On the other hand, the fragile X drug is tested on induced pluripotent stem cells (iPSCs) obtained from patients and fibroblasts that have been reprogrammed to IPSCs and then differentiated in neurons – again, because animal models of FXS don’t exist.
“The model is very robust because it takes into account all the defects that we can find in the patients’ cells, including the hypermethylation of this gene locus,” said Amabile.
Aptadir’s drugs: a new targeted approach
What makes this new class of drugs stand out is how targeted an approach it is. While there are drugs for MDS that have been approved by U.S. and European regulators, they tend to come with a load of side effects. These include drugs like azacitidine and cytarabine, which are hypomethylating agents. These medicines aim to reverse DNA methylation but do so in all types of cells and not solely cancer cells.
“The issue with these compounds is that basically, they are very toxic,” added Amabile. “Unfortunately, many patients are not able to tolerate the therapy because, of course, they become severely affected by lack of platelets, and so, they have to interrupt the therapy. And eventually, these MDS progress to leukemia.”
Aptadir’s MDS drug comprises an RNA molecule that inhibits DNMT1 and specific lipid nanoparticles that can recognize the myeloid compartment – the part of the immune system made up of a variety of cells that originate from the bone marrow.
“We are developing a precision medicine approach in order to deliver the RNA inhibitor only in the cell types that are affected by this defect of methylation without affecting any other organ.”
And in FXS, the technology is the same, with the only difference being that the lipid nanoparticles target neurons and can deliver the RNA inhibitor in order to reactivate the genes specifically in the neurons.
The seed funding will fuel proof of concept studies as well as determine suitable dosage for a phase 1 study. Currently in the midst of identifying potential biomarkers, the team at Aptadir will soon begin manufacturing risk assessment to ensure that its lead asset can be scaled up during the manufacturing and the development of the final drug product. With plans to begin clinical trials in late 2025 or early 2026, Amabile believes that this class of drugs could be a significant stride, particularly in treating children with FXS.
“The hypermethylation in fragile X occurs progressively. So, it is very important to intervene very early during the development in order to have the best chance to reverse the condition by using the RNA inhibitor,” said Amabile.
As it is pretty difficult to reverse a condition wherein 100% of the gene methylated, the focus on treating children, whose genes tend to be 20% to 50% hypermethylated, seems promising.
“We feel even more committed since fragile X is a pediatric condition,” said Amabile. “For us, this is very relevant because we want to bring this to the patients’ community.”