War. What it's good for

To really press his point home, Roberts provided an example from his own mark on history.

“I mean, think of Nixon’s War on Cancer! If it wasn’t for the War on Cancer there never would have been a biotech industry. Really! And we would have never discovered splicing.”

“But did we get an answer to cancer?” he asked. “No...not at all.”

What the war on cancer did do was provide an inspiring puzzle for some of 1970s' brightest and most ambitious scientists. Among them were Roberts and Sharp.

Richard Roberts (l) and Phillip Sharp (r)

CSHL’s Jim Watson was among the scientific sages who realized cancer was a genetic illness, at its roots. Early in the cancer war, though, there was no way to easily study genes, or even know where specific genes were located on chromosomes. Roberts proposed to use a newly discovered class of proteins called restriction enzymes to cut the enormously long DNA molecule into manageable bits that could then be mapped, if slowly, using a manual method. Similarly, Sharp had used the first of such enzymes to sequence parts of the genome of a cancer-causing virus.

One of nature's greatest inventions

Both scientists applied their skills to a basic mystery that molecular biology was then tackling: When an activated gene’s “message” is copied from the original DNA into RNA—the first step in making a protein—how does the RNA message actually form?

Using powerful electron microscopes, Roberts and Sharp both noticed that RNA messages were not precise copies of genes. As they were processed in the cell nucleus, they formed odd shapes and eventually became looped and then broke into smaller pieces, as seen in the background image on this page.

Independently, using some of the same know-how and tools, Sharp's lab (at MIT) and Roberts with his team (at CSHL) soon concluded that a preliminary, raw copy of a gene first had to be edited, or “spliced,” before it could be used to direct protein production.

Chapter 3

A disease of helplessness

Imagine that when you’re born, there is a hand lightly pressing on your chest. At first, it’s difficult to notice; perhaps it only stops you from looking around a room and maybe you have a little less interest in reaching for things. But as time goes on, that hand grows larger and presses down harder. Normally exploring limbs are leaden and breath is pushed from seemingly tiny lungs. You may never learn to sit up. Life with Spinal Muscular Atrophy is not a comfortable one, and if a child is born with a particularly severe version of the genetic disease, it’s a life that won’t last long.

A decade ago, Type 1 SMA would claim a staggering 90 percent of the children born with the affliction each year. Few would make it to their second birthday. Others, somewhat more fortunate, are born with less severe versions. Children with Type 2 SMA usually survive, but only to live with the weight of their own bodies proving too much for their failing muscles. Many lead a breathless, exhausting existence from the confines of a wheelchair.

That is, at least, how it used to be...

“Take that, SMA!”

Today, you might say that SMA has been “beat.”

Approved in the United States and European Union (Japan, Canada, Australia, Switzerland, and Brazil pending), the drug known as nusinersen compensates for the insidious problems within an SMA patient’s genome.

Sold under the brand name SPINRAZA™, the drug has been hailed as the “first-ever treatment for SMA,” and a “huge win” for molecular biology. In fact, SPINRAZA™ was named the "best biotechnology product of 2017" by the prestigious Galien Foundation.

“There has never been a disease-altering therapy for a neurodegenerative disease,” molecular neuroscientist J. Paul Taylor of St. Jude Children's Research Hospital excitedly told Science a few days before the drug became available. (Taylor is not involved with the drug or with the companies behind it.)

But just as the drug’s inventors did, before you can understand how this miracle drug works, you first must understand SMA.

A protein we can’t live without

Working with our friends at Youreka Science, CSHL has created a brief explainer video to help you understand SMA and how nusinersen treats it. We begin with what causes SMA.

SMA is caused by a lack of the aptly named “Survival of Motor Neuron” (SMN) protein. This protein is so important that our muscles cannot develop normally without it.

When a person is born without a properly working SMN1 gene, there’s a serious problem, because it carries instructions for muscle cells to manufacture SMN protein. Deprived of the normal source of vital SMN protein, such a person falls back on a second, nearly identical gene called SMN2. But this gene is flawed. It only makes about 10% of the SMN protein needed by our muscles. These people have Spinal Muscular Atrophy. They usually begin to weaken at the very beginning of life, just as their muscles are developing.

Turning to the backup gene

Once the biological cause of SMA was discovered—a catastrophic flaw in the SMN1 gene—researchers quickly realized that a solution was not going to be easy. Even to this day, there are no approved drugs that repair broken genes. But what about that backup gene we just mentioned? If SMN2 were somehow to become an adequate producer of the vital SMN protein, wouldn’t that halt SMA?

Enter Dr. Adrian Krainer. A curiosity-driven researcher, Krainer’s career has been motivated by his interest in the mechanism of a molecular editing process called RNA splicing that is central in the production of proteins. By the late 1990s—as we describe in Chapter 2—Krainer was known as a master of splicing.

Having worked directly under Nobel laureate Richard Roberts—who co-discovered splicing—Krainer was recognized by the research community as a promising candidate to tackle the RNA problem behind SMA.

“Now suddenly here’s a common disease which I’m learning about in which all the patients have the same defect [in SMN2],” says Krainer. “It was really apparent that if we could find a solution, it would apply to all SMA patients.”

Much of the work Krainer had done as a CSHL Fellow and young lab leader would play a major role in the development of nusinersen. But it would take time to secure funding and introduce others in his lab to the idea of fixing the backup gene, SMN2, as a way of helping SMA patients.

A magical discovery

“It was almost magic—the way things ended up working,” says Dr. Frank Bennett, a leader of drug development at Ionis Pharmaceuticals.

However, Bennett, who was instrumental in nusinersen’s development, knows that it was hard work, not magic, that got the drug to the patients who need it.

“Working with Adrian [Krainer] has been one of my most enjoyable collaborations,” he explains. “It was like two streams of basic research coming together.”

Like most basic research, Krainer’s own stream started as a trickle, but grew into a torrent of insights into the molecular drivers of SMN.

In the late 1980s Krainer had sought to isolate the individual components that made splicing happen. “My first real breakthrough,” he recalls, “was to purify a single protein, which is now called SRSF1.”

An excerpt from Base Pairs episode 5: Dr. Krainer explains how an exhausting method to isolate specific proteins helped him make discoveries that later led to a drug for SMA. See all Base Pairs podcasts.

Later, work in his lab with postdoc Akiya Mayeda determined that SRSF1 is a splicing activator.

As if by fate, it was this same essential activator that Krainer and postdoc Luca Cartegni determined is missing when SMN2’s RNA message is spliced, leading to the problematic skipping of one chunk of its message, called exon 7. Soon after, the pair developed a method called ESSENCE to correct this skipping problem.

And that’s what got Bennett’s attention. There were plenty of kinks to be worked out of ESSENCE, and in 2004, Krainer and the Ionis drug developer worked to optimize the system.

Pleasant surprises

There were more surprises still in store. After Krainer’s identification of SRSF1 as the missing splicing activator that caused exon 7 to be skipped—impairing the SMN2 “backup” gene—he realized that the corrective molecule used in ESSENSE was also able to correct exon skipping when stripped down to a short, “naked” sequence of RNA. Scientists call these tiny sequences antisense oligonucleotides, or ASOs. This was key in the design of the drug called nusinersen. Efforts began to synthesize an ASO with the greatest ability to promote the inclusion of exon 7, that missing part of the SMN2 gene’s message that prevented it from making normal amounts of SMN protein.

From there, things moved quickly. In April 2008, results from mouse trials proved the treatment could correct for SMN2’s major flaw in living cells. Subsequent research even showed that the drug could reverse symptoms of Type 1 SMA, the often fatal form of the disease that we mentioned at the start of this chapter. Soon, Ionis received permission to start testing the drug in people.

By 2015, several pivotal Phase 3 trials were in progress, and one—a trial for infants suffering from SMA—came to a sudden halt. However, it wasn’t disaster that struck. Instead, it was success.

Dr. Krainer describes a key moment during clinical trials that exemplifies nusinersen's success in treating SMA.

Those results were indeed “good enough to convince the FDA,” and in December 2016, the once-experimental treatment became commercially available to SMA patients for the first time.

Meet a superhero

Of course, while wonderful results and FDA approval are successes of their own, Krainer would argue that his biggest success is all the young lives that get to continue thanks to basic research driven by curiosity about how cells work. This was a big dividend.

“When you do the research, you always hope that it's going to have a beneficial impact, but it always seems like that is a distant possibility,” Krainer explains. “It's something you strive for, and now it seems to actually be happening and it's like a dream come true, very rewarding."

Emma Larson was treated with nusinersen during clinical trials. Today, as she and her parents visit Dr. Krainer at Cold Spring Harbor Laboratory, she's stronger than ever!