From UNC: “The Cure Code”

University of North Carolina

July 18th, 2017
Alyssa LaFaro

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Davis can now walk fully unsupported and live a relatively normal life thanks to a correct diagnosis from UNC researchers within the NCGENES project. No image credit.

“Consider this: In 1969, if a disease-linked gene was found in humans, scientists had no simple means to understand the nature of the mutation, no mechanism to compare the altered gene to normal form, and no obvious method to reconstruct the gene mutation in a different organism to study its function. By 1979, that same gene could be shuttled into bacteria, spliced into a viral vector, delivered into the genome of a mammalian cell, cloned, sequenced, and compared to the normal form.” —Siddhartha Mukherjee, “The Gene: An Intimate History”

“I can move my toes,” Elizabeth Davis says.

Her 9-year-old son looks at her in awe. The two stand, wide-eyed in the middle of a Verizon Wireless store in Goldsboro, North Carolina. Davis leans hard against her crutches, staring at her feet. She looks up and smiles.

At age 37 — for the first time in 31 years — Davis can uncurl her toes from a locked position, the symptom of a condition gone misdiagnosed for just as long. Three months later, she sheds her crutches, walking fully unsupported — something she hasn’t done since she was 14 years old.

In 1975, the same year Davis was born, UNC microbiologists Clyde Hutchison and Marshall Edgell experienced a different kind of life-changing event. They’d been working rigorously to isolate DNA within the smallest-known virus at the time, Phi-X174. More than anything, they wanted to understand how to read the genetic code. Then, later that year and across the pond at St. John’s College in Cambridge, Fred Sanger figured it out. The British biochemist became the first person to develop a relatively rapid method for sequencing DNA, a discovery that won him a Nobel Prize in Chemistry — for the second time.

In response to Sanger’s discovery, Hutchison took a sabbatical and headed to England to work in his lab. During his first year there, he helped uncover the entire sequence of Phi-X174 — the first time this had been done for any organism. While there, he realized the new ability to read DNA could help him and Edgell solve a different problem they’d been having back in North Carolina: fusing two pieces of DNA code together to create an entirely different sequence.

After returning to Chapel Hill, Hutchison continued his work with Edgell and also Michael Smith, a researcher at the University of British Columbia who he met while working in Sanger’s lab. Together, the trio successfully fused two differing DNA strands using a more flexible approach to site-directed mutagenesis — a technique that makes gene therapy possible today. They published their results in 1978. Smith would go on to receive the Nobel Prize for this work in 1992.

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The scientific breakthroughs of the 1970s changed the field of genetics forever. In 1980, Sanger received the Nobel Prize for Chemistry for his contributions, along with Walter Gilbert (Harvard), who discovered that individual modules from different genes mix and match to construct entirely new genes; and Paul Berg (Stanford), who developed a technique for splicing recombinant DNA.

Meanwhile, researchers in Chapel Hill continued to chip away at the mysteries of the gene. Oliver Smithies, who came to UNC in 1987, would later win the Nobel Prize for his work in gene targeting using mouse models. That same year, UNC cancer geneticist Michael Swift and team discover the AT gene, which predisposes women to breast cancer; and George McCoy becomes the first clinical trial participant in the world to receive the genetically engineered Factor VIII gene to treat his hemophilia at the then UNC-Thrombosis and Hemostasis Center.

Genetics was changing the world. And this was only the beginning.

An unsolved mystery

One year after Sanger won the Nobel Prize, Elizabeth Davis turned 6. She soon began walking on her toes, which had suddenly, one day, curled under in pain, making it nearly impossible for her to stride with feet flat on the ground. Her knees knocked together as she struggled to move with the swift pace characteristic of a child her age. Davis continued to walk on her toes for years.

“I would even brace the school walls when walking down the hallway,” she says. Eventually, the pain became unbearable. By the time she was 12, she’d resigned herself to crutches.

Doctors believed Davis’ condition could be treated with foot surgery, misdiagnosing her condition for years. By age 14, she had already undergone three procedures — two to lengthen her Achilles tendons and an experimental bone fusion. But each surgery offered little to no relief, and walking only grew more painful for Davis, both physically and emotionally. As her condition worsened, her classmates became cruel — so much so that she dropped out of high school when she was just 16.

By age 20, Davis grew restless. “The pain was constant,” she remembers. “I could hardly move my legs — they just felt weak. I would drag them behind me as I used my crutches. I couldn’t even lift them.” Doctors suggested she undergo a third Achilles tendon lengthening surgery, the result of which minimally improved her condition.

“By that age, I just wanted more,” Davis says. “I just wanted to do things, to go places. I wanted the surgery to work. But it didn’t. And the pain continued.”

It would be another 17 years before doctors realized the problem was hidden in her genome.

The birth of a department

In 1990, the start of the Human Genome Project — an international research program to map out the 20,000 genes that define human beings — further fueled new discoveries in the field of genetics. So when Jeff Houpt, then-UNC School of Medicine dean, formed a research advisory committee in 1997 and asked his faculty what the number-one research program the university needed to focus on, they responded: genetics and genome sciences.

Great minds think alike. At the same time, the College of Arts and Sciences was also hosting its own committee that vied to develop a genetics department. “At this point, I had a vision for a pan-university program,” Houpt shares. “This wasn’t just going to be a program of the medical school.”

Along with the College, the schools of public health, dentistry, pharmacy, nursing, and information and library science all wanted in, offering financial assistance to the program. Then-Provost Robert Shelton and Chancellor James Moeser both signed off on it as well. “What we wanted from Shelton and Moeser was more money and more positions,” Houpt remembers. “And they agreed to that.”

By 2000, a hiring committee was ready to interview candidates to chair the new department and genomics center. Terry Magnuson quickly emerged as the lead candidate. He and his team had spent the past 16 years researching developmental abnormalities using genetics and mouse models, successfully changing the genetic background of a mutated gene.

“It was obvious he was going to have a following,” Houpt remembers. “People were going to listen to him because he’s a good scientist. But more than that, it was pretty clear that Terry was interested in building a program, and this university-wide effort appealed to him.”

Unanswered pain

By the time she reached her 30s, Davis’ condition had spread to her arms. She underwent multiple MRIs, nerve and muscle testing, and a spinal tap. She even endured a fifth, unsuccessful surgery on her feet. Physicians misdiagnosed her yet again. A few believed she suffered from hereditary spastic paraplegia, a genetic condition that causes weakness in the legs and hips. Another told her she had cerebral palsy. “But I didn’t want to believe him,” she says — and it’s a good thing she didn’t.

As Davis continued her search for answers, walking grew more and more painful. “I was always in pain,” she admits. “But some weeks were really, really bad — to the point where I couldn’t even move.” She finally succumbed to the assistance of a wheelchair. “I hated it so much. I barely went anywhere.” And when she did, she needed help.

Her mother assisted her regularly with everyday tasks like grocery shopping. Her youngest son, Alex, learned to expertly navigate her around high school gyms, baseball fields, and the local YMCA pool so she could watch her other son, Myles, compete in the plethora of sports he participated in.

“Myles really experienced the worst of it,” Davis says. “I remember one time, in particular. I was taking a shower and knew I was about to fall. I called for him and he came running. He was always there to pick me back up.”

Sequences and algorithms

After the Human Genome Project published its results in 2004, genomic sequencing became an option for people with undiagnosed diseases. But analyzing and understanding the 3 billion base pairs that make up a person’s genetic identity was an expensive process. As time progressed and technology improved, though, the technique became more manageable for both physicians and patients.

Using these new genomic technologies for outpatient care intrigued UNC geneticists James Evans and Jonathan Berg. In 2009, after gathering enough preliminary data, the NIH granted the team the funds to start the North Carolina Clinical Genomic Evaluation by NextGen Exome Sequencing (NCGENES), which uses whole exome sequencing (WES) to uncover the root cause of undiagnosed diseases. Using just two tablespoons of blood, WES tests 1 percent of the genome — a feat that is both miraculous and controversial, creating a whole new wave of ethical questions.

Simply put: “Some people want information that other people don’t,” Evans explains. Most people want to know about genetic disorders that have treatment options, but when it comes to those that don’t, they’d rather not hear it. “Navigating those different viewpoints can be a challenge,” he says. Privacy and confidentiality also present problems within the insurance world. Although protections exist in the realm of medical insurance, major genetic predispositions could have large implications for life, disability, and long-term care insurance.

Today, upward of 50 researchers from across Carolina participate in NCGENES to study everything from the protection of data to the delivery of results. More than 750 people with undiagnosed diseases have undergone testing.

NCGENES wouldn’t exist without the technical infrastructure that tracks, categorizes, and helps analyze genetic material as it makes its way through multiple laboratories — all of which is provided by UNC’s Renaissance Computing Institute (RENCI). A developer of data science cyberinfrastructure, RENCI provides the software programming that helps the team at NCGENES analyze genomes more effectively.

“You need new computer algorithms to solve new science problems,” RENCI Director Stan Ahalt says. “It takes a multidisciplinary team to understand science problems like genetics — and computer code to make that process go fast.”

A transformative experience

By 2013, Davis was in desperate need of a new algorithm. Thankfully, that year, she was referred to Jane Fan, a pediatric neurologist at UNC. After studying Davis’ file, Fan felt sure that the doctors who tried to diagnose her condition failed, making her the perfect candidate for NCGENES.

Four tubes of blood, 100,000 possible genetic locations, and just over six months later, Fan called Davis. A single gene mutation called GTPCH1 impairs her ability to produce dopa, an amino acid crucial for nervous system function. “I had to hear it in person before I believed it,” Davis admits. “I had been misdiagnosed many times before.”

Not only were UNC geneticist James Evans and his NCGENES team finally able to accurately diagnose Davis, but they were able to treat it — with something as simple as a pill. A pill that has been on the market since 1988, used to treat patients with Parkinson’s disease.

And just like that, Davis ‘life was changed forever by genome sequencing.

Three days after she took one-quarter of a pill, movement returned to her toes while standing in the middle of a Verizon Wireless store in Goldsboro. She began to cry.

Top-five in the country

UNC’s genetics department has ranked in the top-five programs for NIH funding across the nation every year since 2012 (and top-10 each year since 2006). “I think we’ve built one of the best genetics departments in the country,” Magnuson says. In 2016 alone, genetics department faculty brought $38 million to Carolina.

Houpt agrees with Magnuson’s sentiment. “The genetics department is a great example of how universities should run,” he says. “People need to put aside their own interests and see what’s needed. Terry is a leader who’s made each school involved feel like it’s their program and not just a medical school program – which is why he’s now the vice chancellor for research.”

Today, more than 80 faculty members from across campus conduct world-recognized genetics research in multiple disciplines.

Ned Sharpless, for example, focuses on cancer. Most recently, the director of the UNC Lineberger Comprehensive Cancer Center lead a study that paired UNCseq — a genetic sequencing protocol that produces volumes of genetic information from a patient’s tumor — with IBM Watson’s ability to quickly pull information from millions of medical papers. A procedure much too intense and time-consuming for the human mind, this data analysis can help physicians make more informed decisions about patient care.

Another member of Carolina’s Cancer Genetics Program, Charles Perou uses genomics to characterize the diversity of breast cancer tumors — research that helps doctors guarantee patients more individualized care. In 2011, he cofounded GeneCentric, which uses personalized molecular diagnostic assays and targeted drug development to treat cancer.

In 2015, geneticist Aravind Asokan started StrideBio with University of Florida biochemist Mavis Agbandje-McKenna. The gene therapy company develops novel adeno-associated viral (AAV) vector technologies for treating rare diseases. Although still in its infancy, the company has already partnered with CRISPR Therapeutics and received an initial investment from Hatteras Venture Partners. Asokan has spent nearly a decade studying AAV — and even helped to, previously, cofound Bamboo Therapeutics, acquired by Pfizer for $645 million just last year.

In 2016, current genetics department Chair Fernando Pardo-Manuel de Villena challenged both Darwin’s theory of natural selection and Mendel’s law of segregation through researching a mouse gene called R2d2. In doing so, he found that a selfish gene can become fixed in a population of organisms while, at the same time, being detrimental to “reproductive fitness” — a discovery that shows the swiftness at which the genome can change, creating implications for an array of fields from basic biology to agriculture and human health.

A former student of Oliver Smithies, Beverly Koller uses gene targeting in mice to better understand diseases like cystic fibrosis, asthma, and arthritis — research that will ultimately lead to better treatments. Similarly, Mark Heise observes mice to study diseases caused by viruses including infectious arthritis and encephalitis (inflammation of the brain). Both researchers are part of the Collaborative Cross project, a large panel of inbred mouse strains that help map genetic traits — a resource that is UNC lead, according to Magnuson.

Genetics research stems far beyond the UNC School of Medicine. In 2009, for example, chemist Kevin Weeks and his research team decoded the HIV genome, advancing the development of new therapies and treatments. UNC sociologist Gail Henderson runs the Center for Genomics and Society, which provides research and training on ethical, legal, and social implications of genomic research. In 2015, UNC Eshelman School of Pharmacy Dean Bob Blouin helped the school become the first U.S. hub to join the international Structural Genomics Consortium — focused on discovering selective, small molecules and protein kinases to help speed the creation of new medicines for patients.

From crutches to a 5K

After just three months of treatment, Davis walked fully unsupported for the first time since she was 6 years old. She’s since traversed Hershey Park in Pennsylvania, strolled around the World Trade Center in New York, and regularly participated in yoga and spin classes. This past May, she walked her first 5K. “I have crazy endurance,” she says. “When your body feels good, you just want to keep on going.”

Perhaps, more importantly, Davis is able attend Alex’s sports games without assistance. “When I used to walk into the gym on crutches to watch my oldest son play basketball, everyone would look at my crutches and my legs,” she says. “Now, when I go watch my youngest son play, I have so much more confidence walking in to the gym. People see me.”

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