Family enlists Harvard scientists in fight against brain disease — Harvard Gazette

Nina Frost knows that she might be too late to cure her daughter, but she keeps up the fight — one day, her work might transform the life of another child.

Annabel Frost, 10, has a rare condition that triggers seizures severe enough to inflict brain damage, cognitive defects, and movement problems. For Annabel’s first two years, Nina and her husband, Simon, grappled with the condition’s invisible menace as doctors tried and failed to provide an explanation. 

The possibilities ranged from epilepsy to a brain tumor. Maybe, one specialist said, Annabel will just grow out of it. 

“We never know when the next thing is going to strike. We never know how bad it’s going to be.“

Nina Frost

It took a change of scenery — Washington, D.C., to Boston Children’s Hospital — combined with medical serendipity before her condition, alternating hemiplegia of childhood, was diagnosed. 

While the verdict gave the Frosts a name for the illness endangering their child, it brought them little relief. Instead, it clarified the challenges that lie ahead: the difficult road that AHC patients face; how little scientists understand about a genetic condition afflicting only a few thousand people globally; and, most painful of all, how remote the chances of a cure. 

“We have been under assault from Annabel’s disorder for many, many, many years,” Nina said. “We never know when the next thing is going to strike. We never know how bad it’s going to be. We’re constantly on guard and looking out for that.”       

Today, in part due to the Frosts’ efforts, the landscape around AHC has shifted. 

In August, Harvard and Broad Institute researcher David Liu published a groundbreaking paper in which a gene-editing technique developed in his lab in 2019 corrected AHC’s genetic flaws in lab mice. Perhaps more importantly, the mice that received the treatment experienced fewer and less severe seizures, showed improved cognition, and had dramatically longer lifespans. As Liu described it, the mice were “profoundly rescued” from an illness that in humans claims most patients before they reach middle age. 

The techniques detailed by Liu and colleagues have the potential to treat genetic neurological conditions beyond AHC. Frost, who runs a nonprofit focused on AHC and other rare diseases, noted that scientists have documented around 2,000 monogenic disorders of the brain. The list includes Huntington’s disease and Friedreich’s ataxia, as well as familial Parkinson’s disease and some forms of ALS. 

Liu’s team, with collaborators from eight institutions, corrected five different mutations of the disease-causing gene, raising hopes that, rather than a one-off fix, they’ve developed a platform that could be used to rapidly rewrite AHC-related genetic flaws, and potentially those of other conditions. Annabel’s was among the mutations they corrected.  

“The outcome was quite remarkable,” said Liu, the Thomas Dudley Cabot Professor of the Natural Sciences in Harvard’s Department of Chemistry and Chemical Biology. “I’m not aware of anyone previously using prime editing to rescue a neurological disease. We looked at the disease, looked at the most prevalent mutations, and went after several of them with either of the methods that we know of to correct a specific mutation in an animal or a patient, namely base editing and prime editing.”

‘It was severe, and it was scary.’

When Nina Frost rewatches home videos recorded after Annabel’s birth in 2015, she notices early signs of AHC, including the condition’s characteristic nystagmus, or involuntary eye movements. Soon, Annabel began to experience attacks that would strike once or twice a week, leading to paralysis that in the worst cases could last days. Her mother remembers the frequent ambulance rides, and arriving at the hospital only to find that doctors had no idea how to help.

Annabel was 2 when the family traveled from their home in Washington to Boston Children’s Hospital for an appointment with Harvard neurologist Phillip Pearl. Their timing for yet another “second opinion” turned out to be impeccable: Pearl had recently returned from a conference on alternating hemiplegia of childhood. The Frosts brought a video in which Annabel was hooked up to an electroencephalograph, a device that measures brain waves.

“We said, ‘Look, we finally captured a seizure,’” Frost said. “But he’d go to the EEG recording and there’d be no seizure. We’d say, ‘Here’s the video of the same time,’ and there was something that was non-epileptic — but still clearly profound — that was happening to her.” 

Pearl ordered a genetic screen, which found a mutation in ATP1A3, the gene most commonly mutated in AHC. Afterward, the Frosts connected with a community of parents, patients, and scientists that had developed around the disorder. Soon, any doubts they had about Annabel’s condition fell away. Nina still can’t shake the impact of watching a video of a young woman experiencing an AHC seizure. 

“We were looking at a vision of the future that was completely familiar, but really, really severe,” she said. “As soon as we saw the symptoms that she was having on this video, there was no question in our mind: This is the exact disorder that we had. But it was severe, and it was scary.”

Resolved to strengthen AHC science and elevate the priorities of patients and their families, the Frosts founded a nonprofit, now called RARE Hope, to raise money, influence the direction of trials, and serve as a hub for researchers and patients. Their first fundraiser, in 2019, brought in $900,000. 

But all the money in the world wouldn’t help without promising science. In 2021, after Liu used base editing to treat progeria in a mouse study, the family decided to pitch AHC as a model to explore the technique’s ability to cure genetic diseases. 

“We’d been developing different mouse models, and other pieces were beginning to fall into place,” Frost said. “But that was an instance of, ‘We need to make a case for this scientist’ — who’s one of the most incredible scientists in the world, as far as we’re concerned.” 

The Frosts put together a detailed proposal, backed by the knowledge acquired over the years since Annabel’s birth and suggesting collaborators such as Maine-based Jackson Laboratory, which had developed mouse models of two different AHC-related mutations. The proposal was further enriched by the family’s deep connection to the patient community, and their understanding of advances that would have the greatest impact on patients’ lives. Liu was impressed.

Nina and Simon Frost are “two of the most energetic, get-things-done organizers in the rare-disease community space,” he said. “It’s quite amazing to see them operate. They basically pulled together the key participants and then we worked out together a scientific plan that our team executed, in collaboration with the Jackson Laboratory and many others.”

Signs of progress

Most cases of alternating hemiplegia of childhood are caused by mutations in the ATP1A3 gene, which controls the behavior of charge-carrying sodium and potassium ions in nerve cells. The mutation alters signaling in the brain, leading to seizures and paralysis. Some 50 mutations of ATP1A3 are known to contribute to AHC, though just three account for more than 65 percent of AHC cases. 

When Liu’s lab turned its attention to the disease in late 2021, researchers didn’t know exactly what was happening in patients’ brains. The simplest explanation would have been that the mutated gene no longer produced the normal protein — an enzyme that regulates the balance of sodium and potassium ions in nerve cells — and that this deficit caused AHC. If so, traditional gene therapy, which adds an extra copy of a normal gene into the cell to restart production of the normal enzyme, might have been an effective strategy. 

But another possibility was that the mutated gene produced an enzyme that itself had negative effects. In that case, simply restoring the supply of the normal enzyme wouldn’t be enough. Researchers would also have to stop production of the mutant enzyme.

When the team tried traditional gene therapy it had no effect on symptoms, suggesting that AHC was indeed caused by both a lack of the normal enzyme and negative effects from the mutated one. They then deployed their most cutting-edge tool, prime editing, which allowed them to precisely correct the mutated gene, cutting off the flow of the mutated enzyme and restoring production of the normal one.

Alexander Sousa and Holt Sakai, postdocs in Liu’s lab and two of the paper’s first authors, worked first in human cells developed from AHC patients and then in cells from mice with AHC. The results were encouraging, showing that their editing approach efficiently corrected AHC-causing mutations and resulted in virtually no unintended changes elsewhere in the genome. Once that proof of concept was established, Sousa and Sakai connected with Markus Terrey, a study director at Jackson Laboratory’s Rare Disease Translational Center and the paper’s third first author. The three collaborated to test prime editing strategies in mice developed to mimic two AHC mutations. 

Four weeks later, the team confirmed that the prime editor had made the desired changes in the target cells. Now they would have to wait again, this time to evaluate how symptoms were affected. The answer started to emerge after two months, when the control mice began to die. Over the next 10 months, the treated mice experienced fewer seizures, recovered more quickly from the episodes, and showed evidence of improved cognition compared with the controls.

“We knew we’d really done something here,” Sousa said. 

Months later, a second round of treatment, in mice with a different AHC mutation, yielded similar results, an indication that the technique might be applicable to all of AHC’s mutations.

“Seeing that gene editing resulted in rescue for both strains of mice was great because now we can make an argument that this is generalizable between different mutations,” Sousa said. “This is actually really, really, really cool.”

Even so, big gaps remain. The study treated very young mice, leaving open a question that needs to be answered before human trials can begin, according to Cathleen Lutz, co-senior author on the paper and vice president of the Jackson Lab’s Rare Disease Translational Center.

“We’re currently doing the penultimate experiment where we treat mice that have this particular disorder later in their lifetime and ask, ‘Can we get the same effect?’” said Lutz, a frequent collaborator of Liu’s. “I think that will give us some indication of how we enroll and how we look at a clinical trial.”

Long-term thinking

The findings might prove a launching-off point, both for AHC patients and for inroads against other neurological impairments. New collaborations are already being formed, the Liu team says. 

“Looking forward, we’re thinking about even more scalable technologies,” Sakai said. “This is something that we’re working on now to target basically all known mutations in a gene at once, using prime editing.”

“I’m hopeful that we’ll at least have a line of sight to the clinic, that we will know what steps need to be taken to reach patients, within a couple of years.“

David Liu

Though hopeful, Liu is cautious about overpromising a cure for AHC — science is littered with exciting lab results that never translate to patients. His lab is now in the process of planning follow-up studies. If those go well, they’ll move to human trials. 

“That doesn’t mean that the clinical trial will start tomorrow or this year — and perhaps not even next year — but it does mean that we’ve started the process that we hope will ultimately lead to regulatory clearance to conduct a clinical trial to try to directly correct the root cause of this terrible disease,” he said. “I’m hopeful that we’ll at least have a line of sight to the clinic, that we will know what steps need to be taken to reach patients, within a couple of years. That’s the goal.”

What all this means for Annabel, her parents aren’t sure. Despite her condition, she is a happy 10-year-old who, with her 13-year-old sister, Clara, attends the same D.C.-area school their mother attended. She can read and write — math is not a strong suit — and, with the assistance of an aide, attends classes with children her own age. 

“She loves life,” Nina said. “She makes things in our life really rewarding and happy, which is quite fabulous.”

AHC is a merciless illness. Nina believes that prime editing is “truly transformative,” a sign of gene editing’s rapid advance and a source of hope for patients. But it may turn out that the earlier a gene-editing therapy is given, the better. Decades of living with the condition takes a toll that even the most successful gene therapy might not be able to reverse. 

Accordingly, RARE Hope is seeking a potential treatment on more than one front, including through AI-enabled analysis of existing drugs. The larger vision, Nina said, is that Annabel be the inspiration for a relentless effort to help as many patients as possible. 

“We’re thinking about patients across the age spectrum — and Annabel is growing through that spectrum,” she said. “There are the really young who might benefit the most from a genetic type of therapeutic. Then there are the older patients, who might benefit most from a repurposed drug that minimizes some of the episodes but doesn’t necessarily touch the full range of symptoms. We’ve thought from the beginning that it would be worthwhile to develop many different paths to a better life for patients, and that’s what we’re trying to do.”