CRISPR Gene Editing Outpaces Gene Therapy: The Groundbreaking Case of KJ Muldoon

Nine-month-old KJ Muldoon made global headlines following a report in The New England Journal of Medicine, from Kiran Musunuru and Becca Ahrens-Nicklas and their team at Children’s Hospital of Philadelphia and Penn Medicine. They used a highly precise form of CRISPR gene editing to correct a mutation – swapping out one DNA base for another – that lay behind the boy’s inability to break down proteins in food.

Left unchecked, ammonia would have accumulated to toxic levels in KJ’s bloodstream, which would have rapidly lead to organ failure and, ultimately, brain swelling and coma. He was hospitalized until he received the new treatment, kept on a very low protein diet.

The boy inherited one mutation from each parent, and so he couldn’t produce a crucial enzyme, carbamoyl phosphate synthetase 1 (CPS-1 deficiency). The condition affects only 1 in 800,000 to 1,300,000 newborns, and it is quickly fatal in half of them.

KJ was too young for the only treatment, a liver transplant. He received the groundbreaking new treatments in February, March, and April, delivered intravenously in lipid nanoparticles (tiny fatty bubbles) that went to his liver.

“We’ve been in the thick of this since KJ was born, and our whole world’s been revolving around this little guy and his stay in the hospital,” his father, Kyle Muldoon, said. “We’re so excited to be able to finally be together at home so that KJ can be with his siblings, and we can finally take a deep breath.”

KJ is the first case of halting an ultrarare genetic disease using the gene editing tool CRISPR to correct a specific, possibly unique mutation by replacing a single DNA base. FDA has approved use of CRISPR to treat two blood conditions (sickle cell disease and beta thalassemia), but the thousands of patients have the same mutations. Families with ultra-rare diseases tend to be left behind.

Rare disease families are looking to KJ’s story as a sign of hope that medicine will shift to a more personalized mode, based on correcting genetic glitches. Harnessing CRISPR is much more efficient and targeted than conventional gene therapy, which has been around since the 1990s. My 2012 book The Forever Fix: Gene Therapy and the Boy Who Saved It chronicles that history.

From Gene Therapy to Gene Editing
Gene therapy, as envisioned since the late 1950s, delivers working copies of genes into cells, but doesn’t precisely direct them to mutations – a little like a plane circling above an airport and landing at random, compared to a plane setting down on a specific runway. CRISPR, based on a defense system of bacteria, made that specificity a reality.

Gene editing via CRISPR is more like deploying a weapon-bearing drone than dropping a megabomb on a city. The variation used in KJ’s treatment is called a “base editor” – it swaps in a guanine DNA base for an adenine at a precise point in the mutant gene. It’s a little like correcting a typo that alters the meaning of a sentence.

Tailoring gene delivery to a precise location in the genome of a single patient is called “bespoke” gene therapy. “Bespoke” is a term borrowed from tailoring clothing, meaning “made for a particular user.” Personalized medicine is also called “N-of-1,” (or N=1) which refers to an experimental sample size of just one patient.

The power of gene editing over traditional gene therapy is especially meaningful for me, because my book was overly optimistic. I predicted off-the-shelf gene therapies able to treat many conditions, many patients. That, of course, hasn’t happened.

But my book was published on the cusp of CRISPR (see A Conversation with CRISPR-Cas9 Inventors Charpentier and Doudna). Gene editing is technically simpler than “conventional” gene therapy that slips needed DNA into a cell, typically aboard a virus, without directing it to a spot in the genome that needs fixing.

CRISPR Adds Precision
Imagine gene therapy as a Door Dash delivery deposited in the lobby of an apartment complex; gene editing via CRISPR is delivery inside a specific apartment, the bag of food placed on a specific table.

A few gene therapies have been approved by regulatory agencies in the US and Europe since 2012. But some were too costly to survive the medical marketplace, such as million-dollar Glybera, which treats pancreatitis.

Others gene therapies haven’t been approved because they do not improve symptoms sufficiently.

A boy who received gene therapy, twice, for the neurological condition Canavan disease regained eyesight and retained intellect and awareness, yet didn’t survive past early adulthood from other effects in the brain. Some children who have received gene therapy for other complex neurological disorders are living longer than expected, but with some symptoms persisting and perhaps not worsening, but not reversing.

But advances in technology have prevented problems that arose in conventional gene therapy clinical trials.

CRISPR had been retooled to minimize “off-target effects,” in which introduced DNA plops down where unintended, causing a new problem. In a gene therapy trial for an immune deficiency, such an effect caused leukemia in a few boys. And CRISPR trials include immunosuppressants, a lesson learned from 18-year-old Jesse Gelsinger, who died in a 1999 clinical trial of a gene therapy for a urea cycle disorder different from the one KJ inherited. His immune response to the viruses carrying the healing genes had gone into overdrive.

Newborn Genome Sequencing Identifies Patients for Gene Editing
The loss of eight young lives revealed the importance of identifying a single-gene condition before symptoms begin. That is the goal of newborn genome sequencing.

A few drops of blood sampled from a newborn’s heel is tested for dozens of diseases, many caused by mutations in single genes. Newborn screening has been done for decades, typically detecting abnormal levels of metabolites, but DNA tests have been incorporated. An ultra rare brain condition, metachromatic leukodystrophy (MLD), proved the value of knowing a child has inherited a condition from birth. MLD is so rare – 1 in 40,000 to 1 in 160,000 – that it isn’t on newborn screening panels. So children couldn’t participate in clinical trials until symptoms enabled physicians to diagnose them – when it was too late to help.

But Alessandra Biffi, MD, at the San Raffaele Telethon Institute for Gene Therapy in Milan, had a brilliant idea. She began a clinical trial in 2011 to test newborn siblings of affected children, who each faced the 1 in 4 chance of having inherited the recessive disease. The team developed and tested a gene therapy, which worked. The treatment, Lenmeldy, is now available.

But the 2016 Lancet paper describing how the gene therapy works ends with the stunning statement:

“In memory of Baily, Valentina, Carlos, Dennis, Liviana, Mustafa, Randa, and Amany.”

The eight children died, as their younger siblings, who’d inherited the same disease, lived.

Newborn screening in the US still doesn’t include MLD, but some states test for KJ’s disease.

CODA and Kudos
Perhaps the most important part of the success story (so far) of KJ is that he is a proof-of-concept, evidence that the base editing strategy works. An editorial by Peter Marks in the NEJM accompanying the new report, Progress in the Development of N-of-1 Therapy, explains the adaptability of the platform technology that could be applied to any number of rare disorders, at far less cost than traditional gene therapy.

(The widely-respected Dr. Marks, an oncologist and hemotologist, was forced to resign as director of the Center for Biologics Evaluation and Research at FDA in March.)

In a second Editorial, Andrea L. Gropman of St Jude Children’s Research Hospital and Alexis C. Komor from UCSD write that the work “is a milestone in the evolution of personalized therapies for rare and ultrarare inborn errors of metabolism.”

Finally, a news release from (what’s left of) the NIH lists the challenges development of the new treatment had to overcome:
• The gene is too big to fit in a conventional gene therapy viral vector
• Liver cells, where the delivery homes, divide so often that a conventional gene therapy vector would be diluted
• The disease is so rare that there aren’t natural history studies to compare progress among patients.
• Symptoms are very variable, even among individuals with the same mutation.

Summed up Kiran Musunuru:
“We want each and every patient to have the potential to experience the same results we saw in this first patient, and we hope that other academic investigators will replicate this method for many rare diseases and give many patients a fair shot at living a healthy life. The promise of gene therapy that we’ve heard about for decades is coming to fruition, and it’s going to utterly transform the way we approach medicine.”