At a glance: 

  • A collaboration between a computational lab and a translational genomics lab at HMS has propelled research on a novel therapy for frontotemporal dementia
  • The researchers have designed a short, lab-made genetic sequence called an antisense oligonucleotide (ASO) that could become the basis of a therapy for a genetic form of frontotemporal dementia
  • In lab and animal experiments, the ASO appears to boost levels of a protein deficient in the brains of people with this form of frontotemporal dementia

Newswise — It started with a hunt for lab space and ended with a collaboration born out of what the researchers call a “cosmic coincidence.” 

In 2018, Peter Park, professor of biomedical informatics in the Blavatnik Institute at HMS, reached out to his childhood friend and longtime colleague Tim Yu, HMS associate professor of pediatrics at Boston Children’s Hospital. Park’s request was straightforward: Could Yu spare a lab bench to test an idea for a new therapy for frontotemporal dementia (FTD)? Yu did one better. Park wanted to design a therapy based on short, lab-made genetic sequences called antisense oligonucleotides (ASOs) — and Yu and his team had spent the past six months learning everything they could about ASOs as they raced to build a drug for a little girl with a rare neurodegenerative disease.

“We just said, ‘gosh, we need to work together on this’ — and so that’s how the project started,” Yu recalled.

“It was an incredibly fortunate coincidence,” Park added.

Now, five years later, Park, Yu, and their teams have developed an ASO that has shown early signs of promise in lab and animal experiments: The molecule appears to increase levels of progranulin, a protein whose production is reduced in the brains of people with the type of FTD that arises from a mutation in a specific gene.  

To be sure, a lot more work is needed to turn the ASO into a drug that can be safely tested on humans in clinical trials — but its very existence demonstrates the lightning-quick pace at which therapeutics research can advance when scientists with complementary expertise work together.

Moreover, the work contributes to a growing field of research on ASOs, which are the basis of a new class of therapies that may be especially useful for treating thorny neurodegenerative diseases and other conditions that stem from genetic mutations, including certain types of cancer and epilepsy.

Building momentum

In recent years, scientists have become increasingly interested in the therapeutic potential of ASOs, which are short, single-strand sequences of synthetic DNA or RNA built in the lab. The idea is that researchers design an ASO to correct specific protein deficiencies or malfunctions by binding to a particular stretch of RNA transcribed from the gene of interest. This binding can cause the gene to be expressed at higher or lower levels, thus affecting the production of proteins linked to various physiologic functions.

Perhaps the most well-known ASO to date is a drug called nusinersen, which was approved by the Food and Drug Administration for spinal muscular atrophy in 2016. Patients with spinal muscular atrophy have a mutation on both copies of their survival motor neuron 1 (SMN1) gene, which causes reduced production of the associated survival motor neuron (SMN) protein. SMN is the essential fuel for motor neurons in the brain stem and spinal cord that control voluntary muscle movement. The protein deficiency causes patients to experience profound muscle weakness and absence or loss of muscle function that gets worse over time.

Nusinersen is injected into the spine and travels to the brain, where it binds to a section of RNA transcribed from the SMN2 gene in brain cells. SMN2 is closely related to SMN1 but typically produces only a small amount of SMN protein. Once it binds, nusinersen causes SMN2 to produce more of the protein, thus compensating for what the SMN1 mutation suppresses.

“Nusinersen was an overwhelming success — it was extremely effective in these patients — and so a lot of people became very excited about ASO technology,” Park said.

One of those people was Yu, who wondered whether he could design an ASO to treat Mila, a six-year-old girl with a rare, fatal neurodegenerative disease called Batten disease. Yu and his team figured out that in her case, the disease was caused by a known mutation on one copy of the neuronal ceroid lipofuscinosis 7 (CLN7) gene, combined with another mutation on the other copy of the gene. As a result of this duo of mutations, the child’s body could not produce enough of the CLN7 protein, leading to widespread — and worsening — nervous system problems, including seizures, poor coordination and balance, and muscle spasms and weakness.

In a matter of months, the researchers were able to create and test a personalized ASO called milasen that targeted the second gene mutation responsible for her disease. As they had hoped, Mila’s symptoms improved during treatment: she had fewer seizures and she was better able to swallow and hold up her neck and body. Mila died in 2021, but the researchers published their results in The New England Journal of Medicine as proof of concept that it was possible to create a safe and effective personalized ASO quickly.   

The stars align

Meanwhile, Park and his research fellow at the time, Jinkuk Kim, were embarking on a journey of their own. As a computational biologist, Park develops algorithms that analyze human genomes and look for interesting anomalies or trends — something he had been doing mostly in the context of cancer. However, Jinkuk had an interest in ASOs and, more specifically, in finding gene mutations linked to neurodegenerative diseases that could be good targets.

Kim and Park began using their computational tools to analyze human brain sequences publicly available through the National Institutes of Health. They were looking for something specific: genes in which a mutation on only one copy (versus both copies) is enough to alter protein production and interfere with normal function. Eventually, they hit on GRN, a gene in which a single mutation on one copy causes brain cells to make less of a protein called progranulin. Crucially, this GRN mutation is implicated in around 15 percent of cases of FTD — a form of dementia often diagnosed in patients between 45 and 65 years old characterized by a loss of cells in the frontal and temporal lobes of the brain.

“We had the idea that we could design an ASO that would impact the transcript of this gene in such a way that progranulin production would increase,” Park said. However, he and Kim knew that they needed to take their idea out of the computer and into the lab for testing — so Park reached out to his old friend Yu.

When the researchers met to discuss the project, Kim asked Yu if he had ever heard of a drug called nusinersen. Yu couldn’t help but laugh at the sheer serendipity of the situation. “I said, ‘actually, I’ve been doing nothing but studying nusinersen as quickly as I can for the last six months, because we are working on making a drug like it for our patient,’” Yu recalled.

Off and running

With that, Park, Kim, Yu, and Yu’s research fellow Yu-Han Huang threw themselves into developing molecules to target the gene responsible for a significant number of FTD cases. “We began taking these skills that we were learning about ASOs and thinking about how we could apply them to this situation,” Yu said. Their early progress was aided by a $250,000 grant from the Quadrangle Fund for Advancing and Seeding Translational Research at HMS.

Over the past few years, the researchers developed several ASOs that seem promising. These molecules don’t bind to RNA transcribed from the mutated copy of the GRN gene that interferes with progranulin production. Instead, they attach to RNA made from the remaining healthy copy of the gene and by doing so, correct a natural inefficiency in progranulin processing.

“Our strategy is to boost progranulin output from the normal copy of the gene,” to make up for the lack of progranulin produced by the mutated copy, Huang said.

This strategy is particularly appealing, Yu added, because it means that the ASO does not need to be tailored to each patient’s specific mutation, as was the case for milasen, which was designed to target a mutation present in a single patient.

In human cells, the ASOs designed by the team have successfully increased progranulin expression. Testing in mice would typically be the next step, but mice don’t have the genetic sequences targeted by the molecules. Instead, the researchers moved to nonhuman primates, which have the same natural inefficiency in progranulin processing as humans.

“We felt confident enough with our initial analysis that we thought we should try these ASOs in primates,” Park said.

Bolstered by $1 million in funding from a 2020 Blavatnik Therapeutics Challenge Award, a primate study is ongoing. So far, one ASO has been tested in one animal at different timepoints and doses. The molecule does not seem to be toxic and appears to alter the GRN gene as expected. There are also signs that the ASO increases progranulin production in the brain, although the researchers are working on developing better ways to measure protein levels. The molecule needs to be tested in more primates, the researchers cautioned, and they also plan to test the other ASOs they designed, but the results so far seem promising.

“The ASO seems to work as well in a primate as was demonstrated in human cell lines,” Yu said. “This gets you pretty far along the path of what it takes to move something towards the clinic.”

If the primate study continues to yield the desired outcomes, the researchers plan to move on to testing the ASO in clinical trials with humans. The ASO would not only need to alter the GRN gene and increase progranulin levels, but, most importantly, to have a functional effect on patients with FTD. The ultimate yardstick of success, Yu said, would be demonstrable slowing of disease progression.  

“Most likely, a treatment like this would be a potential way to keep the disease from progressing further,” Yu said.

More to come

The chance to work on a therapy has been especially rewarding for Park, who typically spends his time on the computational side of things, far removed from the clinic.

“We always consider how the algorithms that we develop might have some tangible impact, and this is a situation where we went from looking at genomic data to identifying the molecule and doing primate experiments in a very short time,” Park said. “We typically think of a pharmaceutical company spending many years to develop a drug, but here, a single brilliant postdoctoral fellow at a computer used publicly available data to come up with a promising drug candidate in only a few weeks.”

The researchers remain excited about the ASOs they designed, both for their potential to become drugs for FTD, as well as for their contribution to a growing class of novel therapies. The ASOs will continue to be developed by a company set to launch later this year.

ASOs offer several advantages as therapies, Park said. They can be injected directly into the spine, which allows them to easily enter the brain without having to traverse the near-impenetrable blood–brain barrier that prevents so many medications from reaching their targets in the brain. Also, unlike the gene-editing tool CRISPR, ASOs don’t permanently alter a patient’s DNA, which means doses can be adjusted to a patient’s changing needs over time.

Park noted that the GRN gene their ASOs target may also play a role in neurodegenerative diseases beyond FTD, including amyotrophic lateral sclerosis (ALS) and Alzheimer's.

Moreover, it may be possible to develop similar ASOs for neurodegenerative diseases or developmental conditions driven by other mutations that affect only a single gene copy.

“The question is whether you can pull this molecular trick for other neurologic gene targets,” Yu said. “One of the broader avenues for future research is exploring if this strategy can be recycled and applied to other conditions.”

The speed at which the project progressed was largely a result of a collaboration across multiple labs and areas of expertise. For Yu it also highlights the promise of gene-targeting treatments.

“Taking an idea and advancing it this far this quickly really does point out how promising this technology is. Our ASO is not a clinical drug yet — there are a lot more steps — but we showed that the concept and the strategy are robust,” Yu said. “The story is as much about this process for making these genetically targeted therapies as it is about this particular ASO for this particular disease.”

And while the story is far from over, the researchers hope that what started as an idea and a fortuitously timed collaboration will, in the end, be life-changing for patients.