Professional Documents
Culture Documents
Personalized Medicine Is Having Its Day
Personalized Medicine Is Having Its Day
Personalized Medicine Is Having Its Day
https://doi.org/10.1038/s41587-023-01724-9
Personalized medicine is
having its day
From made-to-order genetic therapies to model organisms engineered to be ‘patient avatars’,
the technology exists right now to save patients with rare diseases. By Caroline Seydel
L
ast October, Susannah Rosen, an the corner had finally been turned when a pushing to apply personalized CRISPR thera-
8-year-old girl with a devastating custom-designed ASO made its clinical debut pies more broadly, but regulators remain cau-
neurodegenerative genetic disease, at Boston Children’s Hospital. Researchers tious. Once gene editing is performed, it can’t
took her first dose of a custom-made there, led by Tim Yu, developed an ASO drug be reversed if adverse events arise.
genetic medicine. What’s more, she called milasen to treat a child — Mila — who had Another way that CRISPR can contribute is
got it at no cost, provided by the non-profit a one-of-a-kind genetic disorder. Incredibly, by creating models for drug repurposing stud-
foundation n-Lorem. The drug isn’t gene that drug was designed, manufactured and ies. By genetically modifying yeast or other
therapy: it doesn’t change Susannah’s genome administered in less than a year1. model organisms to mimic a patient’s muta-
or undo her mutation. It’s an antisense oligo- ASOs are only one approach to design- tion, researchers can screen existing drugs to
nucleotide (ASO), a short sequence of modi- ing N-of-1 drugs; CRISPR gene editing, an see whether any address the defect causing a
Credit: PM Images / DigitalVision / Getty
fied DNA, designed to bind to a problematic inherently customizable tool, is moving suc- single patient’s disease.
mRNA transcript and stop production of the cessfully into the clinic, making it another What all these strategies have in com-
disease-causing protein. promising candidate. Clinical trials underway mon is the issue of cost. Without a large cus-
Susannah joins a small but growing group for genetic diseases including sickle cell ane- tomer base to buy the resulting treatments,
of patients who have received treatments mia and congenital blindness, though these scientists working on rare diseases are
designed just for them, called ‘N of 1’ thera- are not ultra-rare conditions, nonetheless struggling to build new models that enable
pies. Personalized medicine seemed to be just have demonstrated that the technique can access to life-saving treatments for all who
around the corner for decades, but in 2018, be used safely in humans. Some people are need them.
nature biotechnology
News feature
Balancing safety with speed not treating outweighs the risk of treating,” the transcript. “People say [cryptic splicing
ASOs aren’t new; the US Food and Drug Admin- says Jonathan Watts of the RNA Therapeutics mutations] are very rare, but the reality is
istration (FDA) approved the first, fomivirsen, Institute at the University of Massachusetts they’re probably not that rare, it’s just really
in 1998. Developed as an antiviral against cyto- Medical School. difficult to find them,” says Aartsma-Rus.
megalovirus retinitis in people with AIDS, Yu points out that the ethical issues around Aartsma-Rus serves as chair of the Dutch
fomivirsen provided a proof-of-concept for personalized ASOs aren’t unique. “Through Center for RNA Therapeutics, a nonprofit
clinical ASOs. It would be 15 years before these guidances, we are seeing concepts that consortium of medical centers developing
antisense drugs began to take off. Since 2013, are already in clinical practice and regulatory personalized RNA therapies. Identifying an
however, no fewer than eight ASO drugs have practice in fields like oncology, where patients appropriate mutation is just the first issue,
been green-lighted for use in the United States who have failed first, second, third, fourth she says (Fig. 1). Ideally, one would want to
or Europe to treat genetic diseases2, including line therapy are often first subjects in very apply it to a disease that affects the brain or
Spinraza (nusinersen), the first FDA-approved early stage, investigational trials of quite new the eye — someplace the ASO can be injected
therapy for spinal muscular atrophy (SMA), agents,” Yu says. “Patients and their clinicians locally. “You can use a very low amount, and
a motor neuron disease that, in its most severe weigh their decisions to participate in these you don’t have to worry about systemic expo-
form, causes death by age two. trials knowing their disease is fatal and other sure,” she says. She adds that there must be
Spinraza’s development, like that of so options have been exhausted.” some hope of benefit to the patient at the time
many therapeutics, was a multi-year odyssey, Regulatory policies differ between the of treatment. “You can do local injection in the
beginning in 2004 and not ending until the United States and Europe, points out Anne- eye, but if someone is totally blind, you can
drug won approval in 2016. In contrast, the mieke Aartsma-Rus, a translational geneti- restore the protein, but they will stay blind,”
milasen story showed that the timeline can cist at Leiden University Medical Center in she says. “You’re not going to return function
be accelerated. Because Mila’s disease was the Netherlands, and this affects what types into the cells. If the disease is too advanced,
progressive and fatal, the risks of waiting a of mutations are eligible for N-of-1 designa- the patient won’t benefit.” The ultimate deci-
year for animal safety studies outweighed the tion. “There’s two things you can do with ASOs: sion rests with the patient, she emphasizes. It’s
danger of possible adverse effects from the restore a protein or reduce the production of critically important that the patient and the
treatment, so Mila began treatment while the a toxic protein,” she says. An ASO that treats family understand realistically what benefits
animal safety study was still in progress. Her a disease by reducing a toxic protein could they can expect and the treatment risks.
treatment was authorized by the FDA under conceivably work for anyone who makes it,
an expanded-access protocol, which allows regardless of the specific mutation. “You can N of 1 … and another, and another
a patient with a life-threatening condition to develop it for one individual, but you know it Unlike in Europe, in the United States “N of
be treated with an investigational drug out- applies to others,” explains Aartsma-Rus. “In 1” can mean “N of 1 at a time.” Jacifusen is an
side of clinical trials. However, exactly where the US, you are allowed to say ‘we’re going to ASO designed against the FUS gene (RNA
to draw the line between letting a child suf- develop this in an N-of-1 setting’, but in Europe, binding protein fused in sarcoma), which,
fer from a degenerative disease and trying a they would say no, it’s not allowed. You either when mutated, causes an aggressive form of
potentially harmful experimental treatment do it for everyone who’s eligible, or not at all — amyotrophic lateral sclerosis (ALS). It’s named
remains a subject of vigorous debate. In a not for one specific patient who happens to be for Jaci Hermstad, who in 2019 became the
2019 editorial in the New England Journal of able to fund that.” first patient to receive the drug, but it wasn’t
Medicine, the same issue where the develop- Milasen is an exon-skipping ASO. It is designed specifically for her. The drug was
ment of milasen was published, Janet Wood- designed to bind to a mis-spliced section of already being developed by Ionis and collabo-
cock and Peter Marks at the FDA raised issues the mRNA for MSFD8 that interferes with the rators at Columbia University and had shown
about how to proceed safely, arguing that production of a lysosomal transporter protein efficacy in a Fus-mutant mouse model5 when
“even in rapidly progressing, fatal illnesses, needed for neuronal survival in an ultra-rare Hermstad received her diagnosis at age 25.
precipitating severe complications or death is form of Batten disease (a late infantile neu- Her twin sister, Alex, had died of the disease
not acceptable”3. ronal ceroid lipofuscinosis, CLN7)4. “A cryptic when she was 17, and, terrified of losing their
Since then, the FDA has published a splicing mutation leads to the inclusion of part remaining daughter, Jaci’s parents launched
non-binding guidance document for investi- of an intron in the messenger RNA, and that a campaign to get permission from the FDA
gators developing personalized ASO drugs. It disrupts protein production,” Aartsma-Rus for Jaci to try the drug, even though it hadn’t
lays out protocols for dose escalation sched- explains. “If you can skip that cryptic exon, yet been tested in humans. At the time Jaci’s
ules, regular safety assessments, and the the normal transcript is back, you can restore disease was diagnosed, the FDA had not yet
establishment of stopping criteria in case of the normal protein.” A properly designed ASO released their draft guidance around the use
serious adverse events. The document explic- can do just that: neutralize a cryptic exon, of individualized ASOs in patients.
itly does not address the level of preclinical restoring the normal transcript. Thus, she “The FDA were extremely responsive,
data or drug quality requirements needed to says, these types of mutations are the most thoughtful, reasonable partners in this,” says
start treating a patient, and it also excludes promising avenue for N-of-1 therapies because Neil Shneider of Columbia, who developed
drugs intended for commercial marketing. cryptic splicing mutations are unique and the jacifusen. “Their goal was clearly to protect
“You can make a really strongly ethical case tailor-made ASO will work in only one patient. my patient but at the same time recognize
that if something is safe in rats, and a patient However, mutations occurring in introns are the desperate nature of the disease and the
is going to die, or is going to lose neurons, it’s difficult to identify because introns contain a risks the disease presented to her.” Although
a better move for that patient to proceed than lot of sequence variability. It’s not always obvi- Shneider had limited toxicity data on
to wait for a monkey study, because the risk of ous whether a particular variant is disrupting jacifusen, the drug was chemically similar to
nature biotechnology
News feature
nature biotechnology
News feature
Giving away ASOs for free the technology enables researchers to create
Stanley Crooke, founder of Ionis, recognizing yeast or worm models with genetic errors that
that the traditional for-profit pharma com- match those in the patients, thus creating a
pany model couldn’t support developing personalized resource for high-throughput
N-of-1 ASOs, founded the n-Lorem Founda- screening of small-molecule drug candidates.
tion in 2020. n-Lorem’s mission is to provide “You don’t program the medicine, like in the
experimental ASO treatments to people ASO model; you program the yeast model,”
with genetic diseases that affect fewer than explains Ethan Perlstein, CEO and founder of
30 patients worldwide. The foundation was Perlara, a public benefit corporation (Box 1).
launched with personal funding from Crooke “What has a faster path to the clinic than even
and Rosanne Crooke, his wife, plus $3.4 mil- a customized ASO? A repurposed drug that
lion from Ionis and $1.75 million from Biogen. already has a safety record.”
Crooke says that other companies are stepping Perlstein says the idea behind Perlara is to
up to contribute as well. “We’ve had wonderful “productize” drug repurposing by using exist-
response,” Crooke says. “Really every vendor ing yeast, worm and fly models. The company
in the oligonucleotide industry is giving either is actually on its second iteration, having been
free or deeply discounted work, and often cash founded originally in 2014 before shutting
donations as well.” They’ve also received dona- its doors in 2019 because of lack of funding.
tions from disease advocacy organizations. Yet some important unfinished business lin-
Crooke also has kind words for the FDA in gered. For two years, Perlara had been work-
terms of how they’ve handled the personalized ing with Maggie’s Cure, an LLC formed by the
therapies. “Being fast is important. Being high family of Maggie Carmichael. Maggie has a
quality is even more important. And it’s the congenital disorder of glycosylation (CDG),
Tim Yu of Boston Children’s Hospital is combination of the efficiency and versatility PMM2-CDG, that affects multiple organ sys-
helping to create a centralized resource of antisense technology with the special guid- tems. Researchers working with Perlara were
to help streamline ASO development for ance that the FDA has issued for the treatment already screening yeast and worm models of
N-of-1 diseases. of nano-rare patients with ASOs that allow us Maggie’s disease, looking for a drug that might
to move as fast as we are,” he says. be effective. The project continued after the
At the same time, he resists the idea that company officially closed, and in January
the platform to have a therapeutic index that n-Lorem should contribute their data to the 2020, Maggie began a drug called epalrestat
was ten times greater, it would be so much N1C efforts. Pointing out that Ionis has been under the supervision of doctors at the Mayo
easier to do single-patient drugs.” The way to “perfecting” ASO technology since 1989, he Clinic in Rochester, Minnesota. The drug is
get there, Watts says, is through collaboration says it wouldn’t make sense to compare their not FDA-approved for any indication, but it is
and sharing of data. data with that of others just starting out. approved in Japan as a treatment for diabetic
N1C also sponsors workshops to help the “We offer to collaborate with basically every neuropathy. Since she began taking epalrestat,
field develop consensus on certain best investigator who approaches us,” he says. Maggie’s motor skills have improved and her
practices, including guidelines for mutation “Our collaborations are that we design and vocabulary has grown dramatically.
selection, preclinical testing, safety tests, reg- make the ASOs, and then we bring an optimal Around the time that Maggie was starting on
ulatory issues, and metrics to define how well ASO forward, and then the investigator treats epalrestat, another family was searching for
a treatment is working. The organization also the patient.” answers for their son’s CDG. Jake Carroll was
serves as a resource for doctors who might not Crooke expressed support for the idea of diagnosed with Man1b1-CDG in early 2020,
have experience in genetic therapies. Last year establishing databases, as long as minimum and his parents, Claire Fast and Matt Carroll,
the group published consensus guidelines6 standards for preclinical testing processes and soon discovered how little was known about
for designing and testing ASOs, and they are performance are defined and rigorous clinical the disease. “It was quite a helpless feeling,”
putting together an online database of con- evaluation protocols with well-defined clinical Fast says. “Very few people in the world know
trol ASOs confirmed to work well in various endpoints are agreed on. “As such, n-Lorem about this disorder.” The Carrolls met the
cell types. is open to contributing data to the N=1 Col- Carmichaels in a Facebook group for families
“A lot of clinicians might have a patient with laborative or other data platforms as appro- affected by CDG, and that’s when they learned
Credit: Michael Goderre, Boston Children’s Hospital
a rare disease and want to help, but don’t have priate,” he says. But, because N1C pools data about Perlara. In 2022, Perlstein connected the
any idea how to approach the FDA. Where do from different investigators all using different family with Clement Chow at the University
you find a source of oligonucleotide for under methods to make ASOs, Crooke says, “one of of Utah. Chow works on CDGs in fruit flies,
$500,000? For a single patient?” Watts says. the worries that I have is that this is being taken and he agreed to conduct a screen for Man1b1
“Sharing information and help, guidance and on by people who don’t really understand drugs in flies.
resources and protocols around all of those this technology.” “We were so desperate at that point,”
kinds of questions is another thing that the Fast recalls. “Learning about what Perlara
more clinically minded people in the collabo- Mining for hidden gems was doing was very exciting for us, just to
rative do for each other.” ASOs are not the only route to N-of-1 therapies. find somebody who knew how to navigate
One major player in ASOs has so far declined CRISPR can help people with ultra-rare dis- the research. It’s really hard to know where
to share data in the collaborative: n-Lorem. eases. Rather than changing a patient’s DNA, to start.”
nature biotechnology
News feature
Box 1
Chow’s fly models did not carry an exact and both teams identified the same biochemi- Chris Boshoff. “At the moment, it only con-
replica of Jake’s mutation, but rather a general cal pathway. Within a week of starting her drug sists of a preclinical component. There are
Man1b1 knockdown made using RNA inter- regimen, Lucy took her first unassisted step. two funding opportunity announcements
ference (RNAi). “In the future, we may want The vast collection of small-molecule drugs for projects up to and including an IND filing.”
to move toward making more personalized that have already been safety-tested repre- A clinical network is in development and pro-
models, using CRISPR to put in real patient sents an underutilized resource that can be jected to be up and running sometime in 2023,
mutations, but that takes so much more time,” mined for cures. “We’re banking on being he says. “That will really change the dynamics
he says. “We can order up all the reagents to do able to find all these hidden gems amongst of this program. We hope it will provide almost
this RNAi knockdown experiment right after the things we’ve already approved as safe,” a seamless transition from preclinical to clini-
the call with the patients, get the reagents says Chow. “I think that it will work for a large cal, and a streamlined access process. If appli-
within a week, have a few tests done in about number of diseases. There’s just so much biol- cants already have an IND, they don’t have to
three weeks, and then it’s off to the races. If we ogy hidden in these drugs. Most of them, we go through the same lengthy application pro-
do CRISPR, it’s months before we even have a don’t really have a good sense of the exact cess for funding.” The clinical network data-
fly we can test.” mechanism of action.” base will also serve as a data sharing resource,
As of January 2023, the screen has identified Perlstein says he has around 30 clients which can help other researchers. “Even if it’s
several drugs, and the next step will be to sit looking for treatments. “Drug repurposing is as small as just sharing a clinical trial protocol,
down as a team and discuss how to proceed. going to go exponential soon,” Perlstein pre- or sharing assays during development, it’s a
“About 20% of the hits we found in our screen dicts. “What were these few N-of-1s is going to start,” Boshoff says.
all fell into the same category, so that was become a tide of N-of-1s. And, of course, that’s No projects have been funded so far, but
really encouraging,” Chow says. “A number of what they talk about with ASOs, that’s what Boshoff says the scope of the program encom-
them either have a pretty good history in pedi- n-Lorem is meant to accommodate, and the passes any gene-based or transcript-directed
atric administration or they’re actually OTC N=1 Collaborative. They’re trying to get ahead technology, including ASOs, gene editing, or
[over the counter].” Once a drug is selected, of this tsunami. And it’s coming.” classical AAV-based gene therapy, provided
theoretically, Jake could begin treatment they address ultra-rare neurological diseases.
right away. Indeed, another Perlara patient Can rare disease drugs be profitable? In a recent New York Times editorial,
named Lucy, who suffers from a different CDG, One year ago, the US National Institutes Fyodor Urnov, scientific director at the Innova-
PGAP3, received her first dose 48 hours after of Health (NIH) launched its Ultra-rare tive Genomics Institute and professor at the
her yeast screen was completed. In that case, Gene-based Therapy (URGenT) program University of California Berkeley, suggested
the family was working with two labs in paral- to accelerate the clinical development of that for rare diseases, public funding makes
lel: while one performed the yeast screen, the therapies for neurological diseases7. “It’s still more sense than for-profit businesses, point-
other was studying Lucy’s own cultured cells, under construction,” says program director ing to the financial struggles of two flagship
nature biotechnology
News feature
about gene editing for rare disease, we will genetic and biochemical technology required
learn more and more how to safely gene edit to find it is accessible in most modern labs.
for common disease.” It remains to be seen whether rare disease
Meanwhile, taking lessons from his prior drug discovery will be financially sustain-
attempt at industrial biotech, Perlstein able, whether using the Perlara model, which
revived Perlara in late 2021, but this time so far relies on funding from families; the
creating a leaner and stronger company. “It’s n-Lorem model, which draws on corporate
decentralized biotech,” he says. “We offer donations and advocacy organizations; or
a fundamentally different business model, the public-funding scenario proposed by
which is a virtual consultancy.” Perlstein sees Urnov. Other for-profit ventures are spring-
Perlara’s role as accelerating the research ing up to try to accelerate N-of-1 therapies;
to find treatments for patients who would for instance, Julia Vitarello, Mila’s mother,
otherwise remain under the radar of big recently co-founded EveryONE Medicines
pharma. “The whole purpose of the company with investment support from GV and Khosla.
now is to become the Y Combinator for rare “This is the time for rare diseases,” says
diseases,” Perlstein said. “What Y Combinator Chow. “In the next ten years, I think you’ll see
did for overlooked founders, I’m doing the therapies rolling out left and right because
same thing with overlooked families.” it’s just been waiting for the technology to
In its new format, Perlara no longer has a be there.” He points out that rare genetic dis-
permanent, physical lab space or full-time eases are far simpler to model in the lab than
employees; it has dispensed with them in complex multifactorial conditions like heart
Six-year-old Jake Carroll has an ultra-rare favor of geographically distributed pop-up disease or cancer. “I think we have all the tools,”
metabolic disorder called Man1b1-CDG. labs and “cure guides” who work as independ- he says. “What’s lacking is the funding.”
Perlara helped his parents find a researcher ent contractors with the company. “It’s kind
who could make a fruit fly model of his of like Uber,” quips Perlstein, “except that Caroline Seydel
disease for drug screening. instead of drivers, I have cure guides.” The Los Angeles, CA, USA.
cure guides get matched with families and
form research teams to develop a personal- Published online: xx xx xxxx
gene therapy companies, bluebird bio and ized treatment, much as Chow’s lab took on
Editas Medicine, as evidence8. By contrast, Jake Carroll’s case.
References
he says, “the California Institute for Regen- For now, Perlstein acknowledges, families 1. Kim, J. et al. N. Engl. J. Med. 381, 1644–1652 (2019).
erative Medicine has consistently and vig- working with Perlara are largely self-financed. 2. Crooke, S. T. et al. Nat. Rev. Drug Discov. 20, 427–453 (2021).
3. Woodcock, J. & Marks, P. N. Engl. J. Med. 381,
orously supported a path to the clinic for He calls them “the tip of the spear” in the quest 1678–1680 (2019).
experimental therapies including CRISPR” for rare disease treatments, which could ulti- 4. Brudvig, J. J. & Weimer, J. M. J. Clin. Invest. https://doi.org/
and is the only such state-funded program mately become available to other patients. 10.1172/JCI157820 (2022).
5. Korobeynikov, V. A., Lyashchenko, A. K., Blanco-Redondo,
to do so. At the federal level, he says, the NIH “I’m not trying to make something that only B., Jafar-Nejad, P. & Shneider, N. A. Nat. Med. 28,
offers funding for academic researchers to benefits the 1%,” he said. “But I’m not going 104–116 (2022).
develop CRISPR-based medicines. “I think to ignore the fact that they exist.” Indeed, 6. Aartsma-Rus, A. et al. Nucleic Acid Ther. https://doi.org/
10.1089/nat.2022.0060 (2022).
this is exactly the right approach,” he says. Maggie’s success with epalrestat led to the 7. Schor, N. F., Tamiz, A. P., Koroshetz, W. J., NINDS Ultra-Rare
“The federal government’s investment in launch in December 2022 of a 40-person Gene-based Therapy (URGenT) Working Group & Broome,
establishing the feasibility of CRISPR cures, phase 3 clinical trial. Without the Carmichaels’ A.-M. Nat. Biotechnol. 39, 1497–1499 (2021).
8. Urnov, F. New York Times https://www.nytimes.
I think, ultimately will benefit the taxpayers. efforts, epalrestat’s benefits for CDGs may com/2022/12/09/opinion/crispr-gene-editing-cures.html
Why? Because as we learn more and more have remained unknown, even though the (9 December 2022).
Credit: Carroll family
nature biotechnology