Personalized medicine has taken a big step forward with the launch of non-profit n-Lorem Foundation, which will create patient-tailored antisense oligonucleotide (ASO) therapeutics for people with rare diseases at no cost to the patients. This comes at the same time as custom gene therapies for rare disease patients are being developed, including some combined with CRISPR. As a result, more people—even those with ultra-rare diseases—could finally have access to treatments.
The process of developing these treatments is still burdensome and expensive. Only a few patients will benefit at first. But this concept has only been a dream until now, with most of these patients being completely shut out of the typical drug development process. What’s more, the scientists and sponsors pioneering these approaches are hoping to create blueprints for the treatment of ultra-rare diseases in general.
“One of the goals is to create a replicable protocol,” said Simon Frost, the father of Annabel Frost, a child who suffers from the ultra-rare disease alternating hemiplegia of childhood (AHC). “We want to do it for our disease, and then take that process and give it to more patients across many more diseases.” Frost, who is CEO of Tiber Capital Group, has been in discussions with multiple labs and investigating several approaches, including ASOs, gene editing, and gene therapy.
The blueprint for the ASO-based approach was a made-to-order treatment for a child with Batten’s disease, a rare neurodegenerative disorder. In 2018, Timothy Yu, a doctor at Boston Children’s Hospital, sequenced the genome in then six-year-old Mila to diagnose the condition. It turned out Mila had a retrotransposon which had inserted into her CLN7 gene. That aberration was blocking normal protein production by that gene.
Yu’s team then created a tailor-made ASO, which they called “milasen”, to mask the mutation in Mila’s genome, as detailed last year in the New England Journal of Medicine. It took about one year from sequencing to delivery of the therapy. Then, nine months after her treatment began, Mila’s doctors reported being hopeful about her prognosis, although they noted that she may already have experienced substantial effects from the disease. Hundreds of people, including parents and researchers, have since reached out to Yu to try and have this process replicated. Yu’s lab is reportedly developing several more personalized oligos, including ones for a rare form of epilepsy and ataxia-telangiectasia, which is a neurological disease.
Addressing the challenges
The demand for more custom ASOs is intense. But there are many issues standing in the way of such therapies.
“ASOs are at the point where the investment in the technology has paid off commercially,” said Art Krieg, an expert in oligonucleotide therapeutics as well as founder and chief scientific officer of Checkmate Pharmaceuticals. “And now Tim Yu has shown the process for making customized ASOs. The questions is whether you can standardize that and could companies find it profitable to develop those therapies.” Further, ASOs only block mutations and need to be given for life.
n-Lorem is funded with $1.5 million from Ionis (formerly Isis) Pharmaceuticals, another $1.5 million from Ionis’s founder and former CEO Stanley Crooke and his wife Rosanne Crooke (a researcher at Ionis), $1 million from Biogen, and additional funds from other donors. Crooke started Ionis in 1989, as a pioneer in RNA-targeted therapeutics. Today, the company has three drugs on the market and more than 30 in development for a wide range of conditions. Biogen is partnered with Ionis on several of these.
Biogen declined to comment for this article, but sent this statement: “Antisense oligonucleotides have been a game changer in the treatment of spinal muscular atrophy (SMA) and we believe they could hold promise in tackling other diseases. So, we are pleased to help support the establishment of n-Lorem Foundation and their mission to provide advanced, experimental RNA-targeted medicines free of charge to patients with ultra-rare diseases.”
“I knew we could do this and I knew there was a need,” said Crooke, who started working on n-Lorem two years ago. But he also realized it was going to be challenging. “The patients need a full genomic workup, and you need an investigator who can submit the IND and oversee it,” he said. One major development that convinced Crooke the concept was feasible was the 2014 establishment of the Undiagnosed Diseases Network (UDN), a research study funded by the National Institutes of Health Common Fund. The UDN comprises clinical and research experts from across the U.S. who work to solve medical mysteries. As of 2019, 12 UDN clinical sites were open.
While UDN will be a key source of qualified patients, Crooke says n-Lorem will not be restricted to those. “We announced the launch last week, and we already have six proposals for patients to treat.” But patients need a confirmed genetic diagnosis and treating physicians. Then they must submit a “proposal to treat” to n-Lorem’s Access to Treatment Committee.
Another critical issue is the FDA’s response. Crooke said he has already approached regulators and they are supportive. But n-of-1 trials like these raise special issues. In an editorial that accompanied the Yu team’s report in NEJM, FDA regulators point out the many challenges to evaluating n-of-1 drugs “…what are the differences between treating one, ten, or thousands of patients?” they asked.
But they also acknowledge that the field is moving ahead rapidly. “Academic clinician–investigators now have the capacity to rapidly uncover specific mutations and pinpoint the putative mechanisms leading to certain rare disease phenotypes. “Various ASOs or other compounds can be produced by third parties, and investigators can evaluate them using in vitro assays or animal models,” the regulators wrote. FDA is holding a workshop in March on individualized therapies to try and advance thinking around this topic.
Ionis’s long experience with ASOs should help in this regard. There are several generations, or classes, of ASOs that the company has developed over the last 30 years. “Many years ago I began putting together integrative safety databases about the different classes of ASOs we have developed,” Crooke says. Each class has generally similar properties, but they also have important differences such has ligands that work in different organs. Ionis has published on these databases and the properties they reveal, as well as providing the FDA access to the databases. That doesn’t mean, however, that researchers will be able to predict all the effects of any ASO in any patient.
Finally, there is the question of cost, which is a particular boondoggle for rare diseases. “We know this is feasible but we want to reduce the costs as far as we can,” Crooke says. n-Lorem and Biogen are both already working on processes to further cut costs, “But we will need to raise even more money to help more patients,” he added. “Patients shouldn’t have to be on the internet raising funds for this.”
While he’s aware of the challenges, Crooke said he’s “feeling optimistic. I’ve been overwhelmingly impressed with the commitment and advice we’ve gotten from physicians, experts on antisense and clinical trials,and others.” He also hopes more modalities, besides ASOs will be able to work with n-Lorem and start similar endeavors. “I’m hopeful a gene therapy company can join us or do the same thing,” he noted.
Gene therapy too
While there is nothing equal to n-Lorem yet, other researchers are already pursuing customized gene therapies, even for patients who have mutations that are very rare or that are not correctable with standardized gene therapy.
Monkol Lek, for example, is a geneticist at Yale who has been working on a gene therapy for a single patient with an ultra-rare mutation in a muscular dystrophy gene. There are more than 30 types of muscular dystrophy, and some are caused by mutations that affect different genes or varying sections within those genes. Lek himself has limb-girdle muscular dystrophy (MD). When he was first diagnosed, he remembers hearing over and over again that there were no treatments for his condition.
That was enough to inspire Lek to leave a career in IT while in his 20s and obtain degrees in physiology, bioinformatics, and genetics. Soon after he arrived at Yale in 2018, Lek met Rich Horgan, founder of the non-profit Cure Rare Disease, and whose younger brother Terry has a type of MD. Lek analyzed Terry’s genomic data, and found he is missing the dystrophin gene’s promoter region, which needs to be activated in order for that protein to be made. Terry is also missing part of exon 1, which is also necessary to generate the production of dystrophin.
While they originally considered using ASOs, Rich Horgan and Lek realized that wasn’t feasible because rather than needing to turn off a gene, they needed to turn on a gene, or at least it’s promoter.
One twist in this particular case is that people have two alternative versions, or isoforms, of this promoter and exon 1—one set in muscle cells and another in brain cells. With that in mind, Lek is using a modified version of CRISPR called “no-cut” CRISPR to introduce a transcription activator attached to the Cas9 enzyme to turn on the brain-specific set, and thus make up for the deficit in muscle. He uses an AAV and CRISPR activation construct as well as guide RNA to direct the CRISPR to the right spot in the DNA.
Lek has already tested his putative therapy on Terry’s cells and successfully corrected the mutated gene in the lab. Next, the treatment will be tested in mice. However, Lek is also exploring the possibility of an “n-of-1” clinical trial – in which the therapy would only be tested in Terry or anyone with his specific mutation.
Rich Horgan’s Cure Rare Disease group is now leading new projects for two boys with different forms of Duchenne MD as well as a patient with the limb girdle form of the disease.
Frost, meanwhile, is still investigating the best options for treating his daughter Annabel. His family has spent $250,000 so far and he expects it will cost another $250,000 to $500,000 to reach “proof of concept.” Annabel’s mutation is in ATP1A3, a gene that is associated with at least 12 different rare diseases (See table). However, Annabel’s specific mutation is very rare. “We’re not sure yet how many of these other conditions would be treated by the same transgene, but it could be a large proportion,” Frost said.
Krieg noted that we are not yet at the point where any for profit company will want to develop n-of-1 therapies. “It doesn’t cost that much to manufacture DNA, and it’s a fully automated process,” he said. It has taken billions of dollars already to get the technology this far and develop applications for some more common diseases. But the overall cost of lifetime treatment is still prohibitive. “Right now, I don’t know why any company would want to do this,” he added. “But there will come a time when there are the right incentives and someone will try it.”
For families such as Annabel Frost’s, these developments are still encouraging, and give them hope that they can help shape the future of the new field of n-of-1 therapeutics. This also supports the idea that more children should undergo whole genome sequencing as soon after birth as possible. With many rare diseases, the damage is compounded the longer the child is untreated. Further, greater understanding of how the full range of possible mutations in any gene impact health, and how that can be treated, will press the field forward.