Diagnosis, At Last
Cara Greene, just turned two, rocks on a toy fire engine at a park near Duke University Medical Center. “I’m riding on a fire truck,” she exclaims with joy, raising her hands in the air.
Just four months earlier, Cara’s arms were practically paralyzed. Her parents and doctors were baffled as to how to help her. A research study led by Duke geneticists David Goldstein, PhD, and Vandana Shashi, MD, changed that.
Cara is just one child the Duke team has helped using next-generation genetic testing. By sequencing only the genes that actually code for proteins (the exome, which is where most genetic diseases arise), scientists can save time and expense. Poring over exomes in minute detail has led to answers that have made a big difference in some families’ lives. As a result, Duke has been named one of six clinical sites in the Undiagnosed Diseases Network, sponsored by the National Institutes of Health. Each site will receive grants of about $7.2 million over four years to investigate baffling cases.
Goldstein and Shashi hatched their first collaboration on a drive back from a National Institutes of Health meeting in Washington D.C. Flights to Durham were canceled because of bad weather. The two, who hadn’t met before, rented a car along with Duke psychiatrist Joe McEvoy, PhD. Talking about her clinic, Shashi mentioned her frustration when she had exhausted all of the clinical genetic testing available but still couldn’t find an answer. That happens with about half of the patients seen in most genetics clinics. Goldstein brought up exome sequencing and how it would one day change medicine. They had the whole study planned by the time they got back to Durham.
In late 2013, Cara was a busy toddler pushing her stuffed animals around in a stroller. Just two weeks before Thanksgiving, she had a high fever. Shortly after she recovered, she began having abnormal eye movements—fast back-and-forth and up-and-down motions (nystagmus).
A neuro-ophthalmologist at Duke Eye Center ruled out a brain tumor. Over the next few weeks, Cara’s fingers began trembling while she sat in her high chair trying to pick up food. Her parents, Kristen and Clayton, who lived in Raleigh, North Carolina, at the time, brought her to Duke every week for an appointment or test. Because of the fever that preceded the trouble, pediatric neurologists suspected an autoimmune disease. But none of Cara’s symptoms completely matched the possible diagnoses. Then, in January 2014, a test showed that her retinas weren’t functioning properly. Cara’s doctors admitted her to the hospital. They called in Shashi because the retina abnormality suggested a genetic disorder.
Shashi talked with Kristen and Clayton about sequencing Cara’s exome via a commercial clinical lab. But no one was convinced that the problem was genetic because it had started so suddenly. Maybe the retina test result was a false positive. Cara’s doctors and parents hoped they were on the right track with an autoimmune diagnosis. Cara had been started on a treatment for that—steroids and intravenous immunoglobulin.
When the Greenes next saw Shashi, in February 2014, the treatment had yielded mixed results. Some of Cara’s symptoms would lessen for a week or so, but then they’d come back. And she had new problems. She had begun having trouble swallowing. She could no longer raise her arms to steady herself, so if she stumbled, she would fall flat on her face. Cara became scared to try to walk.
Shashi offered to sequence Cara’s exome as part of the collaboration with Goldstein. Exome testing through a commercial clinical lab would take three to six months, but Shashi could expedite it if it were done at Duke.
A whole team of scientists scoured the exomes of Cara and her parents for clues. After DNA sequencing and computer processing, the scientists ended up with a list of mutations that were possible suspects. Slave Petrovski, PhD, a postdoctoral fellow in Goldstein’s lab, went over the list gene by gene, narrowing it down based on information about Cara’s symptoms and the various genes’ functions. After the list was culled to half a dozen or fewer mutations, the entire team reviewed it. “This is a lot of attention to each individual exome, much more than would be done clinically,” Goldstein says.
Just three weeks after Petrovski began poring over the data, he emailed Shashi. Cara had two mutations in a gene associated with a rare condition called Brown-Vialetto-Van Laere syndrome (BVVLS) that can strike anywhere from infancy to young adulthood. Both of Cara’s mutations would knock out a protein that transports riboflavin (a B vitamin) inside cells. Previously there was no effective treatment for the disorder, but just in the past two years, other researchers have discovered that high doses of riboflavin helped a few patients dramatically.
Because the exome testing was part of a research project, normally the findings would not be presented to the patient’s family until they were confirmed by an independent clinical lab. But even an expedited clinical test would take three weeks. Shashi didn’t want to wait that long. “Cara was continuing to deteriorate,” she says. “We decided we needed to act on this quickly.” The team explained the urgency to the chair of the Institutional Review Board (the organization at Duke that approves research involving human participants), and an exception was granted.
The team gave the Greenes the news that same week, and Shashi prescribed Cara a high dose of riboflavin (1,500 times the daily requirement). Kristen was so eager to do something to help her daughter that she picked up the prescription at the Duke Children’s and gave Cara a dose in the lobby.
Four months after that first dose, Cara is doing much better. She can play again, though she tires easily. She no longer has trouble swallowing, and she’s regained some of the movement in her arms.
“She really likes to stand in front of a full-length mirror and watch herself lift her arms up in the air,” Kristen says. “She looks in the mirror and gives herself a high five.”
Why does such a simple treatment work? Shashi explains that normally, three proteins control riboflavin transport among cells. Cara’s mutations meant that one of those three was missing. The high dose of riboflavin likely floods the two remaining working proteins, so they can pick up the slack.
In other children, BVVLS has progressed so far that the respiratory muscles weaken, requiring use of a respirator. Riboflavin therapy has reversed that for some. Kristen and Clayton are thankful that they found a diagnosis for Cara as soon as they did. They had feared that if Cara’s condition were genetic, there would be little they could do to help her.
“The exome testing saved Cara’s life and is giving her a chance at life again,” Kristen says.
This story originally appeared in the fall 2014 issue of DukeMed Alumni News.