How physicians and scientists teamed up for one little girl born with a deadly form of Batten disease

There was a time when options were limited for patients with ultra-rare diseases like Batten Disease. But through the rapid analysis of extremely large data sets and the growing availability of whole-genome and exome sequencing, it is now possible to use precision tools to develop customized therapies.

In a study released yesterday in the New England Journal of Medicine, a team of researchers, that included scientists from Charles River Laboratories, describe the rapid delivery of a drug to treat 6-year-old Mila Makovec, who was born with neuronal ceroid lipofuscinosis 7 (CLN7) — from a family of inherited rare diseases caused by autosomal recessive genetic mutations. The disease causes seizures, blindness, cognitive decline, ataxia, and is ultimately fatal.

Mila was given a synthetic RNA drug—referred to as an antisense oligonucleotide—that is designed to help her cells ignore the genetic defect that caused CLN7. It is able to do this by binding to defective RNA, hiding it and tricking cells into producing normal protein.

Mila received her first injection in January 2018. According to the study, her seizures have subsequently decreased in both frequency and duration. The seizures once occurred 15-30 times daily, now they occur 0-20 per day and are lasting less than a minute. The clinical data has been corroborated by overnight EEG monitoring, which indicated that both the frequency and duration of seizures decreased by greater than 50%. The study also states that the drug appears to be safe, with no reports of serious adverse events during the first year of treatment.

However, there is no evidence that her neural cells are making the CLN7 gene’s protein, and in fact MRIs showed brain volume loss seven months after treatment, extending a trend that had been observed the previous three years prior to administration of the ASO drug.

Nonetheless, the study did help show that ASOs are a worthy pathway for the rapid delivery of individualized treatments.

According to Mila’s physician, Dr. Timothy Yu, millions of patients in the US are living with rare diseases. Genome sequencing is a useful tool for diagnosis, but that must still be translated into effective therapies. At the Charles River World Congress in September, he said that the promise of turning an ASO into a true drug platform could affect those millions of patients with rare genetic diseases.

Mila’s story also highlights a paradigm shift in the regulatory pathways for rare disease drugs, particularly n=1 drugs that are tailored for one specific patient. Dr. Lauren Black, a Distinguished Scientist with Charles River’s Scientific Advisory Services group, who spent part of her career with the US Food and Drug Administration (FDA), said the preclinical toxicology work done on milasen (so-named for its young patient) was precedent-setting both in terms of the unusually compressed timetable and the regulatory agency’s quick response.

“Ordinarily, [the FDA will] take a three month study and review it before the first dose occurs,” says Dr. Black, who was a co-author of the NEJM study. “This was unacceptable for Mila, because that’s three full months lost. So, I collaborated with [Dr. Yu] on the tactics for working with the FDA. We put the whole proposal in front of the FDA to say: will you allow this?”

A Dire Diagnosis

Mila began to show signs of her disease at 5, when she suddenly went blind and started losing her ability to speak and move. Two years later, her parents learned the reason why. Doctors in Colorado sequenced the protein-coding part of her genome and found an error in one copy of the CLN7 gene (also known as MFSD8.). Normally, both parents need to pass on copies of the defective gene to cause the disease, but in her case only the gene from Mila’s father appeared to be defective.

With Mila rapidly declining, a friend of the family noted on Facebook that Mila needed whole genome sequencing done quickly. A physician at Beth Israel Deaconess Medical Center saw the post and referred it to Dr. Timothy Yu, a neurogeneticist at Boston Children’s Hospital. He generated Mila’s whole genome and noticed that a section within the noncoding portion of her mother’s CLN7 gene didn’t line up properly with the normal sequence for the CLN7 gene. But when drilling down into the sequencing data they detected a retrotransposon —components of DNA that can amplify themselves in a genome and bounce around—had caused an error in the CLN7 gene of the mother.

Given the poor prognosis of children with CLN7 Batten disease—most children die before their teens—and Mila’s clinical condition, Dr. Yu filed for permission from the FDA to initiate clinical investigational treatment under an Expanded Access Investigational New Drug application.

Thinking that an ASO might be able to silence the defective gene, they turned to a company that had used the same technology, and then asked Charles River for help in executing the preclinical studies. It proved to be a whirlwind process.

All hands on deck

Dr. Black was the first person at Charles River to connect with Dr. Yu.

“Essentially, he explained that Batten’s disease was a lysosomal storage type disease, and that if they could get this protein re-expressed, then we could potentially either stop her decline, or possibly even reverse some of the decline that she had recently experienced,” she said in a video interview earlier this year. 

Charles River’s neurologic experts in Kuopio, Finland helped to design the toxicology approach, and its safety assessment site in Montreal performed specialized spinal toxicology studies. One was a biodistribution study in 12 rats and the other was a full toxicology study in 150 rats. Bioanalysts in Ashland developed a rapid chemical method to measure the drug in spinal fluid and tissues. This small rat study was a key puzzle piece, confirming that milasen would last long enough to work in Mila, and also proved that her risky spinal injections could be spaced out.

Charles River’s biologics safety team in Malvern and Woburn kicked into high gear and expedited testing to rule out contaminants and endotoxins—also crucial to Mila’s treatment, as drug products in the final vial must be ultraclean for spinal injection use.

In the end, literally hundreds of employees from Finland, Montreal, Ashland, Malvern and Woburn contributed to the preclinical studies.

“We understood how steep her decline was, and the fact that she was running out of time,” said Dr. Julie Douville, Director of the Infusion Parenteral Administration in Charles River’s Neurotoxicology Department in Montreal and a co-author of the study. “It was very clear that we needed to do everything we could as fast as we could. Even faster than we could, actually, in order to try and not just save her, but minimize the progression of the disease, to dose her as quickly as possible.”

Douville said that there were about 200 people involved in the study in some capacity from the Montreal sites alone, from animal technicians to people in shipping. Each detail of the study had to be perfect to ensure safe and speedy delivery of results, and Douville’s team left no room for error.

“All aspects of it were covered by experts,” she said. “I ran the project myself and we had the Director of Pathology read the slides and the Director of Clinical Pathology analyzed the clinical pathology. We put the best people we had on it because it was so critical to get it right the first time, because there wouldn’t be a second time.”

Dr. Black helped employees at Boston Children’s Hospital present their case to the FDA. The results from all the tests were sent to the FDA in two stages, the last being the final vial testing and the adjusted clinical protocol. Knowing it was coming, the FDA reviewed all the data and approved Mila’s trial within a week.

“When we have a situation where someone needs guidance, and they clearly don’t know what kind of toxicology studies to do, they send it to our group, which is the Scientific Advisory Services group,” said Dr. Black. “That’s what we’re here for. When someone is looking for somebody to give them guidance, I can often cover at least the top layer of what sort of toxicology will need to be done for their particular situation.”

Milasen remains an investigational drug, and because it was tailored for a single individual is not suited for the treatment of other patients.

“Nonetheless, this experience indicates that antisense oligonucleotides may deserve consideration as a platform for the rapid delivery of individualized treatments,” the authors of the NEJM study concluded.

(You can hear more about Mila’s story here. Explore Charles River’s rare disease drug discovery and development platform here. And check out these recent blog posts on clinical applications of ASOs and ASO safety assessment.)