ARTICLE IN BRIEF
In two separate studies and presentations, investigators identified new gene variants implicated in epilepsy.
A group of new studies on the genetics of epileptic encephalopathy (EE) — a severe group of epilepsies characterized by refractory seizures and cognitive arrest or regression, associated with ongoing epileptic activity, that typically carry a poor prognosis — is making it clear just how complex the etiology of this disorder is. Emerging from these studies are new genes, new pathways, and new appreciation for the overlap of EE with other neurodevelopmental disorders, including autism spectrum disorder (ASD) and intellectual disability.
Heather Mefford, MD, PhD, assistant professor of pediatrics at the University of Washington in Seattle, looks for gene mutations using “next generation” sequencing, a technique that allows probing many genes at once.
In a new study presented in December at the American Epilepsy Society meeting in Washington, DC, Dr. Mefford reported the results of this approach in over 600 EE patients, screening for mutations in over 100 genes. The work expanded on her study of more than 500 patients and over 60 genes, published Sept. 12 in Nature Genetics.
“Traditionally — five years ago — sequencing was done on one gene at a time, one exon at a time,” Dr. Mefford explained. While next-generation sequencing is still a long way from sequencing the entire genome, “it allows us to cherry pick sequences for genes we want to study. We can pull out the coding regions of all those genes, and sequence them all at once.”
She chose to look at several classes of genes: genes previously known to cause epilepsy, in order to look at the associated phenotypic spectrum; genes associated with intellectual disability or ASD; and genes she suspected were associated with epilepsy but had never been confirmed as causative.
Overall, she found likely or confirmed disease-causing mutations in 10 percent of the patients. About 15 percent of candidate genes tested that were not previously associated with epilepsy carried likely causative mutations. Three new genes were responsible for disease in more than one patient: chromodomain-helicase-DNA-binding protein 2 (CHD2), synaptic Ras GTPase-activating protein 1 (SYNGAP1), and myocyte-specific enhancer factor 2C (MEF2C). [For more, see “New Genes in Epilepsy.”]
“It [CHD2] is becoming an important gene family,” Dr. Mefford said, “since it gives a new pathway for understanding neurodevelopmental disorders.” A recent study from a European consortium found CHD2 mutations in Dravet syndrome patients without sodium channel mutations, and confirmed its pathogenicity in a zebrafish disease model. Dravet syndrome is a form of EE, characterized by febrile seizures and risk of status epilepticus.
A smaller number of patients in her study carried mutations in MEF2C, another developmental regulatory gene associated with autism. SYNGAP1 is involved in synapse formation, and has previously been implicated in intellectual disability.
The genetic connections and clinical overlap among these neurodevelopmental disorders “is an emerging theme,” Dr. Mefford said, likely due to pleiotropic effects of these genes during development. But not every mutation is associated with such a wide phenotypic spectrum. In her newest study, she found that mutations in GRIN2A, a glutamate receptor subunit, are restricted to epilepsy aphasia syndromes, and mutations in GABRA1, a GABA receptor subunit, are linked only to Dravet syndrome.
“We are finding that there is a lot of genetic heterogeneity in epileptic encephalopathy, probably in part due to the complexity of brain development, and the number of genes involved,” she said. “Little by little, we are getting better at being able to diagnose patients, as we identify these new genetic causes, but I think we are still really at the tip of the iceberg. This is telling us we have a lot more gene discovery to do.”
That complexity also argues for sequencing many genes simultaneously in looking for a diagnosis for most individual epilepsy patients, she said. “It is hard to guess when the patient walks in the door which mutation they are going to have, and therefore which genes to test.”
That message was echoed by another study presented at the meeting, which looked at the results of next-generation sequencing and copy number analysis of 53 genes in 1600 individuals from the data of GeneDx, the genetic testing laboratory.
Researchers found known or predicted pathogenic variants in 16 percent of their sample, with the highest yield in the subset of patients with infantile-onset epilepsy (21 percent). Half of the reported mutations were not in ion channel genes, noted lead author Gabriele Richard, MD, chief medical officer at the company. They included mutations in the Rett syndrome genes — methyl CpG binding protein 2 (MECP2) and cyclin-dependent kinase-like 5 (CDKL5) — along with genes associated with other rare neurodevelopmental disorders. “There is a huge overlap in presentation of all of these genes,” Dr. Richard said, “and that is what makes it so difficult to know a priori which genes you should be looking at.” [For more, see “New Genes in Epilepsy.”]
While targeting multiple known or suspected genes is increasingly common in genetic testing, sequencing the entire “exome,” or coding portion of the genome, is emerging onto the scene at multiple testing labs. “This is not in the future,” she said. “This is reality.” Currently it is used primarily for patients with complex and puzzling phenotypes, but as the price comes down, it is likely to find more utility, especially for disorders such as epilepsy with so many potential causes.
The result of these studies, said Alexander Bassuk, MD, PhD, associate professor of pediatrics at the University of Iowa, who was not involved in the studies, “is that it does not seem that any particular gene is going to be responsible for any significant portion of the genetic cause of severe epilepsy,” highlighting the challenges of using these new discoveries to catalyze therapy development.
But these studies are exciting for a number of reasons, said Dr. Bassuk. “They have shown that next generation sequencing can be used to efficiently screen a large group of patients, for a large number of genes. Combined with other studies, something like twenty percent of the causes of severe epilepsy may be solvable now. They have also further demonstrated the overlap between autism, intellectual disability, and epilepsy.” On the other hand, he said, “Eighty percent of the time, we still don't know what is happening. There is still a lot of work to do.”
“These findings are in line with a number of other recent studies,” said Daniel Lowenstein, MD, professor of neurology at the University of California, San Francisco (UCSF), and director of the UCSF Epilepsy Center. These include the Epi4K study, which performed whole-exome sequencing on over 150 patients with EE. “It is now becoming clear that many cases are due to so-called private mutations,” of which there are likely “many dozens, if not eventually hundreds of mutations in different genes, that can cause the same syndrome.”
“The good news is that we are beginning to get at the actual causes of the disease,” he said. “The challenging news is that therapies may have to be individually tailored,” given the wide variety of mechanisms implicated in the origin of epileptic encephalopathies. “But we are now beginning to talk for the first time of true precision medicine in epilepsy. We now have targets, and functional studies are beginning,” he said, noting a recent high-throughput screen that turned up the antihistamine clemizole as a potential treatment for Dravet syndrome. “I think this is truly the beginning of a new era, where we will be slowly moving through these variants, and finding new compounds.”