“There are at least 2,500 genes that, if mutant, could lead to some type of developmental delay. No physician could have seen that many cases or understand the consequences of them all. Now we can use the power of modern sequencing to diagnose these cases quickly, in one to two weeks.”
“A brand new syndrome”
Most health conditions with genetic components, like cancer or heart disease, emerge from networks of genes interacting with a patient’s environment or lifestyle. By contrast, diseases fated by a mutation in just one gene are individually much rarer but, in aggregate, affect millions of Americans. Many are catastrophic and filled with heartache, as they are currently incurable and predominantly affect children.
The hallmarks of more familiar single-gene conditions, such as sickle cell disease, Tay-Sachs disease and cystic fibrosis, are recognizable to physicians and clinical geneticists, and simple lab tests can confirm them even without whole genome DNA sequencing. But rarer, less-studied syndromes, like the AAA case history referenced earlier, can go undiagnosed or misdiagnosed for years, adding to parents’ anguish and delaying treatments that might alleviate symptoms.
The poignancy of childhood conditions may explain why, when asked what achievement best illustrates UCLA’s leadership in precision medicine, pathologist Braun is unhesitating: “Our effort to molecularly define Mendelian diseases,” he said. Mendelian is the term geneticists use to describe syndromes caused by a single gene. “Previously, it might require years of expensive tests and expensive work-ups to identify these conditions. Now, we can have a patient’s genome sequenced in about two weeks, which often reveals the mutation driving this condition.”
Once a causative mutation is found, however, curing or even just treating single-gene diseases remains enormously challenging, particularly when mutations disrupt normal fetal development or affect numerous tissues. But pediatricians, physicians and parents agree that the earlier children are diagnosed, the better their families will cope with the condition. Diagnostic information is also immediately useful for determining whether other family members are at risk. For many, that diagnosis will require genome sequencing.
At UCLA, diagnostic DNA sequencing for rare diseases is done at the Clinical Genomics Center, founded in 2011 and the second facility in the U.S. after Baylor College of Medicine designated to make next-generation DNA sequencing and data interpretation accessible as a disease diagnosis tool. As head of the center, geneticist Nelson is familiar with many families his group has worked with and counseled over the last five years.
“A common scenario is that a pediatrician or genetics specialist will refer a child for genome sequencing if that child displays symptoms that suggest inherited or progressive disease,” Nelson said. Such genetic conditions of unknown origin are often described as developmental delay. “Usually we sequence Mom and Dad's DNA also to know whether a mutation is inherited or de novo, [meaning spontaneous rather than inherited]. In many cases, we find that a child has a rare but identifiable genetic disease.”
Nelson and his colleagues recently quantified diagnosis accuracy in a paper for the Journal of the American Medical Association reporting results of 814 cases of suspected genetic conditions, many in infants, which were referred to the genomics center from a variety of clinics. The paper reports that “trio sequencing” (of the child and both parents) uncovered a mutation accounting for symptoms in 25percent of the patients analyzed, and in cases of developmental delay as high as 41percent.
And in the rarest cases, genome sequencing has served as a gene discovery tool, as it did in the extraordinary instance of a 4-year-old child analyzed soon after the center opened. Diagnosed with developmental delay, the girl exhibited multiple symptoms, including facial anomalies, microcephaly, heart defects and low muscle tone. Trio sequencing revealed that the child carried a de novo DNA mutation in a gene called KAT6A, which encodes a protein that maintains chromosome structure in many cell types. What was mystifying was that the mutation did not match any documented disease.
“Later, we found three more children with de novo KAT6A mutations in the same place in the gene,” Nelson said. “We then realized we were looking at a brand-new syndrome, something never before described in the medical literature.” By then, the parents of a child harboring the mutation had taken the initiative to reach out over the Internet to parents of children with similar symptoms to encourage them to have their genomes sequenced. “By the time we published our paper about these cases in 2015, the parents had found dozens of families with children carrying similar KAT6A mutations.”
Now there is a KAT6A Foundation with a website dedicated to raising disease awareness and showing families how to navigate territory that is unknown to them and to clinicians. There is no cure for the condition, but on one heartbreaking page of the KAT6A website, the parents of Chloe, the young girl with KAT6A disease who is the face of the site, share minute details of treatments Chloe has undergone, how helpful they were and the names of specialists she saw to help relieve each of her six major symptoms. People who worry that “big data” approaches will rob medicine of the human touch should go to the KAT6A Foundation’s website.
Physicians use the term “evidence-based” to describe patient care decisions, (be they diagnostic or treatment-related, based on systematic analysis of data, as opposed to the advice of a colleague. Genomic diagnosis of extremely rare childhood diseases like KAT6A is irrefutably evidence-based and is in fact a textbook example of how some ends can be achieved only by precision means. “If doctors relied only on their own or colleagues’ experience to make a diagnosis, as has often occurred in the past, then some diagnoses would never be made,” said Geschwind, leader of the UCLA Institute for Precision Health.
Genomic approaches are equally applicable to rare diseases that emerge in adulthood. In 2014 UCLA neurologist Dr. Brent Fogel and colleagues in the genomics center published DNA sequencing analysis of 76 patients with adult-onset undiagnosed movement disorders, or ataxia, in the Journal of the American Medical Association: Neurology. That work identified the causative gene in approximately a quarter of the patients, a breakthrough that earned it accolades from Neurology Today as one of the Best Neurology Advances of 2014.
Geschwind said he envisions a future brought about by insistence on evidence-based precision approaches and less reliance on anecdotal ones. In that future, physicians could check patients’ electronic health records by computer, as many already do, and readily access information relevant to a patient’s gene sequence, clinical characteristics and lifestyle issues, the latter maybe via a patient’s cellphone. The physician would of course be well-versed in manipulating large data sets, having received bioinformatics training in medical school, and could easily compare his or her patient’s record to that of a very large population of similar cases.
“All of a sudden, you might discover 600 patients out of 6 million with characteristics just like your patient,” Geschwind said. “Now you could start to optimize your patient’s care.”
Correcting faulty genes: a “sea change” in precision treatment
One success of genomic medicine is the advent of so-called gene therapies to replace a faulty or mutant gene. In 2014, UCLA investigators made stunning progress in this effort when Dr. Donald Kohn conducted a clinical trial that cured 18 babies harboring a mutant gene that causes the immunodeficiency syndrome called SCID; the trial did so by transferring an undamaged copy of that gene, called ADA, into their blood stem cells.
The promise of whole-gene transfer techniques has led to recent development of next-generation “gene editing” techniques, molecular tricks that could allow one to go beyond simply slotting in a normal gene (as Kohn did to cure SCID), but to repair a defective gene by modifying its A, G, C, or T bases inside a living cell. Gene editing is still not done in humans, and editing strategies aimed at correcting diseases emerging from multiple mutations still seem impractical. A gene repair process is much more feasible, however, when there is only one suspect: “If we are ever going to do gene editing in patients, it will happen in rare, single-gene disease,” Nelson said. “In some cases, if we could change a single base in a gene, we could mitigate these conditions.”
Unfortunately, conditions comparable to KAT6A or AAA syndrome may not be immediately amenable to genetic intervention, not because the mutations that cause them are unrepairable but because they can do developmental damage, often catastrophic, to heart or brain tissues before a child is born. A more attractive candidate for “in-time” gene repair might be a disease (like SCID) in which a single damaged gene wreaks havoc in just one or two tissue types after a child is born.
A candidate that fits that bill is muscular dystrophy, a progressive wasting disease seen only in boys. In its severest form, patients lose mobility in adolescence and die from respiratory failure, often in their mid-twenties. Muscular dystrophy is caused by mutations in one gene, dystrophin, which encodes a protein that protects muscle cells from destruction caused by repeated contraction. As a good candidate for gene therapy, dystrophin is expressed primarily in muscle, so cellular damage generally occurs postnatally in just that tissue. In the minus column, however, dystrophin is the largest gene in the human genome; whole gene transfer techniques like the one used to cure SCID work much better with small genes.
Another complexity is that muscular dystrophy severity depends entirely on where mutations occur along the behemoth dystrophin gene. Normally, dystrophin lies along human chromosome 21 arrayed in 79 segments, like boxcars in a train. Geneticists call these segments “exons.” In in dystrophin, not every boxcar is equally important. If you damage exon 51, for example, the train becomes shorter and patients exhibit a milder, later onset form of the disease. But damage others, such as exon 45, and the cars uncouple, the train jackknifes and patients make little or no protective dystrophin protein. These types of mutations cause the most lethal form of Duchenne muscular dystrophy (DMD).
In addition to leading the genomics center, Nelson is teaming with UCLA scientists to test a genomic DMD therapy that targets only the defective exons, not the entire dystrophin gene. Together with M. Carrie Miceli, a professor of microbiology and molecular genetics and co-director UCLA’s Center for Duchenne Muscular Dystrophy, the group is experimenting with a technique called “exon skipping,” in which one literally tricks cells into skipping over, or ignoring, a mutant dystrophin exon. Clinically, the therapy would be administered by injecting therapeutic gizmos made of RNA called “oligos” into a patient’s muscle tissue, where they recognize and then sideline the defective exon. This is not a gene repair strategy per se; the “corrected” dystrophin protein would be shorter than normal, as it lacks a segment, but in theory it should be functional enough to protect muscle cells from destruction or to lessen disease severity.
This sounds like science fiction, but it isn’t. Two clinical trials recently tested injection of exon-skipping oligos into boys with the DMD exon 51 mutation, in some cases restoring dystrophin levels, albeit in small amounts. Debate over treatment effectiveness continues but, anticipating future trials, Nelson and Miceli are optimizing compounds to co-inject with the oligos to boost their efficiency. In cells from DMD mouse models and in human stem cell models, they work.
Nelson and Miceli are strong proponents of accelerating FDA approval of exon skipping as the first DMD gene therapy. It is not purely an intellectual pursuit: Their son Dylan, 15, has a severe form of DMD and now uses a wheelchair. Dylan’s mutation is not in exon 51, so approval of an exon 51-skipping protocol would not immediately benefit him. It would, however, certainly set the stage for targeting his mutation and that of other children in the near future.
The dystrophin exon-skipping story represents a remarkable promise of genome-based medicine, as about half of the boys diagnosed with DMD harbor mutations in one of nine exons. If successful, the approach would resemble designing an all-purpose rocket to shoot at muscle cells and arming it with nine different warheads targeting chromosomal targets mutant in that subset of patients. Few strategies proposed to target any disease-related gene are as precise, and potentially as versatile, as this.
Despite his personal circumstances and the serious challenges faced by the families he sees at the genomics center, Nelson conveys overwhelming optimism and good cheer, an attitude shared by many of his UCLA colleagues who work on equally serious health concerns. Gloom and doom are not part of a typical day at the center: “Our people enjoy solving complex biological problems and taking care of kids with rare, mysterious diseases,” Nelson said. “Part of the satisfaction is in anticipating where these approaches are taking us.”
It already has taken him far beyond the way things used to be. “Mendelian diseases were traditionally seen as bad luck. Parents were told to treat symptoms and not expect a cure,” he said. “But the prospect for genomic treatments for at least one of these conditions, DMD, is one of the year’s big stories. We are about to undergo a sea change in precision treatment in this arena. We know we can change this mutation.”