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Rare Diseases: Customizing Cures, Patient by Patient

December 17, 2019

Yale geneticist with muscular dystrophy wants to cure a rare form of the disease.

Nearly two decades ago, doctors diagnosed Monkol Lek, PhD, a geneticist at Yale School of Medicine, with limb-girdle muscular dystrophy, a rare, inherited muscle-weakening disease that will eventually rob him of the ability to walk without a cane. At the time, he was otherwise healthy and already a successful IBM computer engineer.

During visits with neurologists in the years that followed, he kept hearing the same refrain: No medicine or treatment could stop his disease. Lek refused to accept this. “I decided I could listen to the experts or go on a journey to find a genetic cure,” Lek says.

So, he quit his job at IBM and re-enrolled in college. He knew he needed to build up a base of knowledge about human biology in order to understand his disease, so he earned a second undergraduate degree in physiology. To make sense of the enormous data sets produced by machines that sequenced DNA, Lek needed to know how to analyze data, so he earned a third degree in bioinformatics. Then, he earned his PhD in medicine, specializing in genetics. All of Lek’s training was aimed at one goal: to investigate—and eventually fix—the exact location of the genetic hiccup causing a disease, including his own. 

A genetic technique quickly grows up

Research assistant Vincent Ho loading a gel cartridge into a 3D bioprinter. “The bioprinter will be used to model patient mutations,” says Lek. “These functional models will allow us to measure the impact that correction of patient mutations will have on various muscle properties.”

Scientists studying the human genome have long known that any mistake in the sequence of chemicals that forms a gene can have debilitating effects on the human body. A gap, or repetition, or deletion in DNA scrambles the body’s basic blueprint of instructions. This can cause cellular-level processes to go awry. A common result of genetic mutations is that proteins that perform crucial roles in the body don’t function properly or aren’t produced at all. In Lek’s case, proteins that support healthy muscles don’t function as they should. 

So, for decades, geneticists and other researchers have worked to develop a way to correct such genetic mistakes. Called gene therapy, this procedure involves placing a corrected gene into some sort of vessel that will distribute it directly into a patient’s cells, each of which has a full copy of the genome in its nucleus. 

Scientists first attempted gene therapy in the early 1990s and believed its application would be widespread in a few years. But that didn’t happen, in part because finding the best delivery vessel—a virus that can slip undetected past the body’s immune system—turned out to be far more complicated than researchers expected.  

When Lek finished his doctorate studies in 2012, the Food and Drug Administration (FDA) had not yet approved any gene therapy treatments. But, now several therapies have been approved and more are in the pipeline. Researchers finally have developed a potential fix for specific genetic mutations. 

And already Lek wants to go a step further. His lab is focused on searching for a way to individualize gene therapy. Many rare disease patients, like himself, have genetic mutations that fall outside of traditional targets that might be correctable with a standardized gene therapy. For example, more than 30 types of muscular dystrophy diseases exist. All are caused by mutations that affect different genes and sometimes even varying sections within those genes. This means that, though two patients might both be diagnosed with MD, their conditions may require different therapies as they could be caused by slightly different types of genetic variants. 

Not long after he arrived to Yale in 2018, Lek found a patient with a rare subtype of muscular dystrophy that has left him bound to a wheelchair. (The patient is taking medications that manage his symptoms but won’t help him regain muscle strength.) Lek sequenced the patient’s DNA to determine exactly which region of his genome is malfunctioning and therefore not producing enough of a type of protein, called dystrophin. While Lek’s ultimate goal is to correct the patient’s genetic mutation, he first needs to design and test a gene therapy in his lab. 

Individualized gene therapy

Lek and his wife, Angela, playing with their dog, Sandy.

In his experiments so far, Lek has combined the use of gene therapy with a gene editing tool called CRISPR. CRISPR is made up of repeated DNA sequences originally found in bacteria that can target and fix genetic mutations in human cells with the help of an enzyme. In its standard form, the tool uses the Cas9 enzyme, which acts like scissors, to cut out problematic DNA sequences. In some conditions, after the DNA is cut, a cell’s own DNA repair mechanisms kicks in to correct genetic malfunctions. 

However, Lek’s patient is already missing a crucial section of DNA, called the promoter region, so this typical approach won’t work. (The promoter region needs to be activated in order for the patient’s gene to “turn on” and make the dystrophin protein.) So, Lek is using a modified version of the tool, called “no-cut” CRISPR, to address the problem. Rather than cut out a problematic sequence, this tool uses a molecule, called a transcription activator, that is attached to the Cas9 enzyme to turn on, or activate, a gene.

“You can think of the gene as dormant, and something has to tell it to wake up and make more protein. Everything’s ready to go; it just needs to be turned on,” Lek says. 

So far, he has tested the therapy on the patient’s cells in Petri dishes in his lab. In that sterile and tightly controlled environment, he successfully corrected a mutated gene. The next step will be testing the therapy in mice. These experiments, which are supported by a research grant from a nonprofit called Cure Rare Disease, could take up to two and a half years. However, since Lek has already shown that the technology works in the lab, he reached out to industry and regulatory experts to find out which parameters need to be met in order to start what’s called an “n-of-1” clinical trial. This means it will be tested only in this patient. He plans to contact the FDA early in 2020 to confirm that the animal experiments will meet its standards in order to show that the therapy is safe to try in humans. 

If Lek’s personalized gene therapy works, it will lay the groundwork for designing personalized therapies for patients with other genetically caused diseases, including himself. 

“As a rare disease patient, I want to see the whole story out,” Lek says. “I don’t want to say to my patients, ‘This is the end of the road for you.’”