Treating genetic disease: Is a cure a cut away?

ONVENTIONAL SURGERY can’t help patients such as Delaney Van Riper, a 19-year-old college student with an independent spirit, love of literature and progressive neurological disease.

But gene surgery might.

In recent weeks, a molecular scalpel began to make test cuts on a troubling mutation in Van Riper’s cells that causes stumbling and weakness in her hands, in hopes of allowing a healthy gene to take over and multiply. While the research is preliminary — her DNA is being changed in the lab, not her body — it’s a step toward fulfilling the therapeutic promise of gene editing, offering a one-time procedure to cure devastating genetic disorders and potentially helping millions of people around the planet.

The pioneering research is underway at Dr. Bruce Conklin’s lab as part of the nascent Genome Surgery Initiative, an effort of the UCSF-UC Berkeley Innovative Genomics Institute to see if our genetic blueprint can be fixed as efficiently and effectively as bones, hearts and other parts of the human body.

“It’s anatomy that we’re cutting out,” explained Conklin, the UCSF and Gladstone Institutes researcher who co-conceived the Initiative and dreams of making gene surgery widely available to the public. “It’s just very small anatomy.”

The precise cutting tool, called CRISPR-Cas9, alters the genetic sequences in cells. It isn’t the first gene-editing method. But it is much faster, cheaper, easier and more accurate than earlier versions.

“It’s like the Model T — not the first car but the one that changed the world,” according to Hank Greely, director of the Center for Law and the Biosciences at Stanford Law School.

Its discovery in 2012 by UC Berkeley’s Jennifer Doudna galvanized the medical community — and now, only five years later, it is moving out of test tubes and toward testing in humans, with clinical trials for various diseases slated to start next year.

But it’s no one-trick pony. Different strategies can be enlisted for different disorders. In some surgeries, such as Delaney’s, CRISPR merely cuts out a bad gene. For diseases such as sickle cell, it must cut, correct and replace.

There’s no guarantee that CRISPR will cure Delaney of the disease that causes her to stumble when she walks or struggle when she opens a bag of shredded cheese. Things that work perfectly in a test tube often fail in the human body. There are concerns about elevating the risk of cancer or cutting DNA in the wrong place. And CRISPR can’t fix medical problems caused by multiple genes, such as heart disease or diabetes.

But here’s the dream: If research succeeds, then one day — not too far away — doctors could build a common “pipeline” of gene therapies, creating the efficiencies and economies of scale needed to cure the estimated 6,000 to 8,000 single-gene disorders afflicting 350 million people around the world.

In support of that vision, Conklin and other innovative Bay Area thinkers are envisioning a path-breaking role for a future Genome Surgery Initiative – a collaboration among UCSF, UC Berkeley and, perhaps, Stanford – that would establish the Bay Area as a center of genetic excellence, spinning off lucrative new innovations.

“We’ve always thought about genetic disease as something which is incurable, something that you’re born with,” said Conklin. “We’ve never really thought about it as something that we could actually cut out or repair.”

“With this new editing tool,” he said, “we can think about how to do this for the very first time.”

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Cutting and pasting

It’s all possible because of stunning advances in genetics.

Life has existed on the planet for 3.5 billion years. But only in the past 65 years – a single human lifetime – have we understood the structure of DNA. Just 15 years ago, we compiled a list of DNA’s 3 billion letters.

And five years ago, we learned how to rewrite it.

Doudna and Emmanuelle Charpentier, then at Umea University in Sweden, demonstrated a way to use CRISPR to slice up any DNA sequence they choose — then add or subtract pieces.

The discovery ignited the imagination of the region’s top scientists and clinicians – Conklin at UCSF and Gladstone, Jacob Corn at UC Berkeley, Matthew Porteus at Stanford and many others.

Meanwhile, it’s gotten faster and simpler to find bad genes. In 2003, it cost $2.7 billion and took 13 years to piece together a sequence of the 3.1 billion units of DNA of the human genome. Now it costs under $1,000 and can take less than one day.

That made it possible to find the rare mutation that hides in Van Riper’s cells.

It happened – like so many other mutations that we all carry in our DNA — soon after the first spark of life, when cells are quickly dividing. Neither of her parents carries the mutation, so it was not inherited.

There was no sign of trouble during her first six years spent in the family’s comfortable Elk Grove home, outside of Sacramento.

“She was rambunctious – a wild child,” said her father AJ Van Riper. “Delaney used to love to do ballet and silly goofball things, walking around the house on tippy toes, prancing around for hours.”

On the eve of her 7th birthday party, while watching her play, something shifted in her father’s mind. Coincidentally, he’s a trained genetic counselor who directs departments at four major Kaiser Permanente facilities in the Sacramento Valley.

“I am looking at what looks like a silly princess, walking on her toes. Suddenly, I shifted from father to genetic counselor,” he recalled. “I thought: ’My daughter is ’toe walking.’ How could I not see that before?” He asked her to walk on her heels. She couldn’t.

“She’s not being silly or goofy,” he said. “She needs help.”

Delaney’s diagnosis: Charcot-Marie-Tooth disease, characterized by progressive muscle degeneration and weakness. One of the most common inherited neurological disorders, it’s also among the most well understood. A stunning 1,000 or more different genetic misspellings can cause symptoms. Delaney’s mutation is called “P182L.”

It’s in a gene that serves as quality control for proteins in nerve cells – essential for the efficient transmission of nerve signals. The gene examines proteins as they’re being made, folding them in the right direction and then passing them on, said Conklin. Proteins have to be perfectly made to do this incredible task of sending signals all the way from the brain to distant fingers and toes.

The mutation means that nerve cells can’t generate the impulse. So muscles atrophy. The nerve signals that must travel the farthest are the most affected. It causes stumbling, and weakness in Delaney’s hands.

Delaney, resilient and resourceful, found ways to thrive. She played recreational soccer until age 13. She learned tumbling, mastering back handsprings. During summer, she babysat triplets.

There were dark years during her adolescence, when she worried that she might someday need braces or casts on her feet. Angry and frustrated, she was tempted to stop everything — the doctors’ appointments, the exercises, the expectations. She wondered, Why am I abnormal? Will anyone love me? Why me?

“Then I realized that getting mad is not going to change it,” she said.

Now a student at UC-Santa Cruz, she’s devised techniques to open jars, close plastic bags, type quickly and stride to class.

It remains frustrating, she admits.

“I can feel myself telling my body to use my muscles, but it doesn’t actually happen. It’s like in a dream: You’re telling yourself to run, but your body can’t,” she said. “You can’t feel your muscles working — but you know you’re telling them what to do.”

Her hopelessness turned a corner when she discovered, from her father, that research was under way — and that she might be able to help.

“I didn’t realize that people were working on it — they were actually looking for a solution,” she said. “It is amazing how far science has come. It is amazing people care about it.”

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Two strategies using CRISPR

Researchers say that Delaney’s disorder is a perfect place to try CRISPR. Our long strands of chromosomes carry two copies of every gene – and only one copy of her gene is bad.

The mutation doesn’t have to be fixed; it just has to be cut out. The cell rejoins the DNA’s cut ends. Then the healthy gene can take over.

Her family drove her to Conklin’s lab at UCSF and Gladstone Institutes, where she donated vials of blood. Her blood cells were turned into stem cells, then nerve cells. Now, using CRISPR, Conklin’s team is testing different places to cut. The final step is to see if the nerve cells are fixed and grow normally.

If it works, Conklin envisions a day when CRISPR might be injected into Delaney’s spine, where the nerve cells live. Then, if healed, the long sensory and motor pathways in arms and legs might start to grow back. And her muscle could strengthen.

The same approach – a simple deletion of the bad part of the gene – also could be used to target other diseases, such as two forms of blindness and a neurological disease called transthyretin amyloidosis.

But other diseases aren’t as straightforward as Delaney’s. It’s not enough to just cut the DNA – you need to repair and replace it.

That’s the strategy used by IGI’s Corn and Stanford’s Porteus to attempt to treat sickle cell disease, a deadly blood disease that affects about 100,000 Americans and millions more worldwide. Sickle cell disease is excruciating and often fatal, caused by a mutation on chromosome 11 that distorts blood cells so they can’t deliver oxygen.

The researchers aim to cut out the mutation in immature blood cells from patients’ bone marrow, then replace it with the correct DNA. The fixed cells would be re-infused back into the bone marrow – and could start making healthy blood. The technique has worked in mice and soon will  enter human trials.

This “repair and replace” approach also is being used by other labs to treat diseases such as Duchenne muscular dystrophy, glycogen storage disease, cystic fibrosis and severe combined immunodeficiency.

And scientists are racing to invent different treatment approaches that borrow from CRISPR’s toolkit. One changes immune system cells so they can better detect and destroy cancer. Another, called “base editing,” fixes mutations by precisely rearranging the bases that make up DNA - not cutting. A third, tested in blood diseases, doesn’t fix the faulty DNA but uses CRISPR to crank up levels of beneficial blood cells.

There remains plenty of worry over side effects. Two new studies earlier this month found that edited cells sometimes lack a functional gene known to prevent cancer. While this doesn’t mean that CRISPR causes cancer, it suggests the need for further research and testing.

There’s also debate over the best ways to get the Cas9 into the body. Modified viruses can do the trick, but other teams are testing electrical surges, nanoparticles and other techniques to move CRISPR across the cell membrane.

For now, diseases of the nervous system, immune system and blood seem to be the best candidates for CRISPR, because work can be done outside the body, said IGI’s Scientific Director for Biomedicine Dr. Alex Marson.

Of these diseases, only those that are well understood, and otherwise incurable, offer strong promise, said Conklin.

“The vast majority of genetic disease … we don’t even have a basic understanding to know what we should do,” he said.

It will take pioneers such as Delaney, perhaps hundreds of thousands of them, to take CRISPR from a provocative tool to a powerful therapy — moving a once-unthinkable feat from the vials and flasks to the bedside.

“If there’s any chance that I can get better, I’ll definitely take that chance,” she said.

“If not, it’s furthering science,” she said, “and hopefully giving other people a chance to be part of this or have a cure for themselves.”