Is Recent Gene Therapy Setback for Duchenne Muscular Dystrophy (DMD) Déjà vu All Over Again?

In the final chapter of my 2012 book The Forever Fix: Gene Therapy and the Boy Who Saved It, I predicted that the technology would soon expand well beyond the rare disease world.

I was overoptimistic. Gene therapy clearly hasn’t had a major impact on health care, offering extremely expensive treatments for a few individuals with rare diseases. We’re still learning possible outcomes of sending millions of altered viruses into a human body. Can they deliver healing genes without triggering an overactive immune response?

A report in the September 28, 2023 The New England Journal of Medicine describes a young man with Duchenne Muscular Dystrophy (DMD) who died just days after receiving gene therapy. The details are disturbingly reminiscent of the famous case of Jesse Gelsinger, who died from a ferocious immune response to experimental gene therapy in September 1999.

Jesse was 19, and had a disorder of the urea cycle (ornithine transcarbamylase deficiency). He was treated on a Monday and died that Friday, as his organs shut down. The viruses used to deliver genes veered off course, entering unintended cell types in the liver that set off immune response alarms.

Gene Therapy Approvals are Still Scant

Although a few hundred people have vision thanks to Luxturna, approved at the end of 2017, the list of gene therapies to pass FDA hurdles remains short. In addition to high cost and small markets, patient responses haven’t been predictable. We need a better way to identify patients most likely to respond to a particular intervention.

Consider Zolgensma, a gene therapy approved in 2019 to treat spinal muscular atrophy. Affected children rarely live past infancy. That’s why videos of a little girl named Evelyn dancing after receiving Zolgensma were astonishing – her sibling died of the disease. But a more recent case was an infant who received the $2.25 million one-and-done gene therapy in 2021 and progressed, by eight months of age, only to being able to keep his head up for a few seconds.

FDA has approved 6 gene therapies, buried in a list of 32 Approved Cellular and Gene Therapy Products. Lumping gene and cell therapies together isn’t very helpful – the cell-based ones are mostly doctored T cells to treat cancer. Two intriguing products are a treatment for knee pain consisting of a patient’s cartilage cells grown on pig collagen and 18 million of the patient’s own fibroblasts injected under the skin to fill out “nasolabial fold wrinkles.”

The approved gene therapies are for:
• The clotting disorders hemophilia A and B
• The severe skin peeling condition dystrophic epidermolysis bullosa
• Retinal blindness
• Spinal muscular atrophy

The sixth is a gene therapy to treat DMD, but only in boys aged 4 to 5 who can still walk. The package insert for the drug, Elevidys, warns of adverse effects of acute liver injury and inflammation around the heart and muscles. It doesn’t mention lung damage, which is what led to the recent death.

Delivering a Giant Gene

The 27-year-old with DMD had inherited a mutation in a gene on the X chromosome from his mother.

The implicated gene is the largest in a human genome, with 2.2 million DNA bases. It encodes the protein dystrophin, which is vanishingly scant compared to the actin and myosin filaments that make up muscle mass, but it functions as a crucial linchpin. Destroy the ability to make dystrophin, as happens in DMD, and skeletal and cardiac muscle fibers fall apart. Muscles stop working. Affected individuals miss parts of the gene or the entire gene.

The DMD gene therapy delivers a shortened version of the dystrophin gene, just 4,558 DNA bases. Two other design strategies add precision.

First, adeno-associated virus (AAV) delivers the genes, rather than the adenovirus (AV) that had entered cells in Jesse’s liver that weren’t the targets. Since his tragic case, use of AV has become more restricted in gene therapy applications and AAV more commonly used as the delivery vector.

The second change is more profound – instead of adding copies of a working gene, as gene therapy when I wrote my book did, this time CRISPR gene editing made it possible to actually fix the mutation. The approach is called custom CRISPR-transactivator therapy. It’s called “custom” because it was designed to edit a specific mutation, with the goal of affecting a sufficient number of the body’s millions of muscle cells to improve mobility, even just a little.

The approach builds upon a peculiarity of the patient. Although his skeletal muscle cells completely lacked the gargantuan dystrophin gene, certain brain neurons retained the start of the gene’s DNA sequence (the promoter and exon 1). So the researchers designed the CRISPR tool to coax the man’s skeletal muscle cells into producing a short version of the needed protein, perhaps enough to provide some function. It had worked in cultured cells and in mice bearing human DMD genes.

A Fast Decline

A team of specialists selected the patient for the tailored clinical trial because of his rapidly worsening situation and the lack of treatments.

Many pre-procedure tests ensued. He didn’t have antibodies to the virus that would be used – AAV9 – nor did he have evidence of any of the viral infections that affect transplant recipients. Cardiac markers were okay. Just to be safe, he received immunosuppressive therapy.

But it seems the immune response didn’t care how well engineered the healing viruses were, nor the many precautions taken.

He was treated October 4, 2022. And then things happened fast.

One day after the gene therapy, the patient experienced premature heartbeats. By day two, a dropping platelet count. By day 3, biomarkers indicated that his heart was beginning to fail.

By day 4, carbon dioxide was building up in his blood, and by day 5, his cardiac function worsened as the sac around the heart filled with fluid.

Day 6 brought acute respiratory distress syndrome (ARDS) and cardiac arrest. He died 2 days later. Despite treating each crisis as it arose, on day 8 he died from multi-organ failure and coma. Autopsy revealed obliterated alveoli – the tiny air sacs in the lungs.

Innate Versus Adaptive Immunity: Two Tiers of Defense

Like Jesse Gelsinger, the man with DMD died too quickly for the reason to be the adaptive immune response – production of B cells and T cells, which typically takes a week or longer. That left a more immediate and generalized innate immune response as the likely culprit.

An immune response is two-tiered. First, the innate response releases general anti-viral biochemicals, like cytokines (such as interferons and interleukins) and proteins called complement. Days later the more precise adaptive response of B cells produces antibodies specific to molecules on the pathogen’s surface as T cells unleash more cytokines and attack directly.

The conclusion: the patient had an innate immune reaction that caused ARDS, attributed to the high dose of the gene therapy. His blood serum was teeming with cytokines that are typically at near-undetectable levels, as his heart drowned. One cytokine, interleukin-6, was 100 times as concentrated around his heart as in the blood. With his heart and lungs under attack, he didn’t stand a chance.

Autopsy revealed AAV9 concentrated in the lungs and liver, but not much in the muscles, the intended target. Nor were there antibodies against AAV9. That picture adds evidence to the timing of the man’s decline that is consistent with the deadly response stemming from innate, and not adaptive, immunity.

The researchers conclusion: the man had a “cytokine-mediated capillary leak syndrome” that sent fluid around the heart on day 5 and into the lungs, triggering deadly ARDS on day 6. “Both host factors and inherent properties of the vector led to unexpectedly high levels of vector genome in the lung and may have contributed to the outcome,” they wrote.

So in addition to trimming genes, carefully choosing vectors, tests galore, and even using more precise new tools like CRISPR, the characteristics of the patient remain a paramount consideration. The lungs of the 27-year-old who died from gene therapy for his muscular dystrophy were, for some reason, prone to infection from the viral vector, the usually safe AAV9.

Perhaps our tools and technologies don’t stand a chance against the forces of evolution.

It’s Hard to Challenge A Billion Years of Evolution

The overactive innate immune response that killed the man with DMD (and is responsible for many COVID deaths) is the more ancient of the two branches of immunity, dating to a billion years ago. We deduce that because it’s present in all multicellular species – animals, plants, and fungi. A biological response that has stood the test of deep time has done so for a reason – it is advantageous, supporting survival. And perhaps that’s one of the limitations of attempting to supplement, replace, or fix mutant genes.

In contrast, the adaptive immune response that pours out antibodies and sends out armies of T cells arose less than 450 million years ago, deduced from its presence only in vertebrates.

And so, ironically, the antiquity of the innate immune response is perhaps the highest hurdle to overcome when using modern biotechnology to attempt to therapeutically alter our genes.