Key Points:

•  As part of its quest to find a cure for the epilepsies, CURE Epilepsy has led initiatives, including one focused on genetic epilepsies.
• The impact of CURE Epilepsy on epilepsy genetics over the years has been broad, ranging from the discovery of individual genes that are associated with epilepsy, to contributions in rare epilepsies, to the Epilepsy Genetics Initiative (EGI).
• In this CURE Epilepsy Discovery, we highlight the efforts of EGI and the centralized database to store and analyze genetic signatures associated with epilepsy; we also summarize its impact on people living with genetic epilepsies and the epilepsy research community.
• We then feature three recent CURE Epilepsy grants awardees who have contributed to numerous aspects of genetic epilepsies ranging from the development and application of new technology to study epilepsy genetics, to studying specific genes and their contributions to epilepsy, to exploring the epigenomic pattern associated with epilepsy.
• The three CURE Epilepsy grants awardees are Dr. Heather Mefford at St. Jude Children’s Research Hospital, and Drs. Gemma Carvill and Jeff Calhoun, both at Northwestern University.
• Adding to this work is a recent endeavor, the Rare Epilepsy Partnership Award to find cures for rare forms of epilepsies.

Deep Dive

Epilepsy occurs when the normal electrical signaling between brain cells (neurons) is disrupted; however, the exact causes of epilepsy are not fully understood. Broadly speaking, epilepsy can have several potential causes, and one of these causes is genetic. Epilepsy is said to have a genetic cause if the seizures are caused as a result of a genetic defect or mutation.[1] These epilepsies are very diverse and the underlying gene or genes involved are not always known. Having a genetic cause for the epilepsies does not necessarily mean that the gene mutation was inherited; sometimes, the genetic variant or mutation may occur spontaneously in a child without being present in either parent; these are called “de novo” mutations.[2] Some epilepsies that have a genetic cause may have additional environmental causes as well.

With the emergence of novel technologies, our knowledge about the genes impacting the epilepsies has grown substantially in the last several years. The increased availability and steadily decreasing costs of genetic technology to analyze one’s entire genetic makeup has meant that scientists can identify many more genes that may be associated with epilepsy. By identifying particular genes associated with epilepsy, we can create animal models to simulate epilepsy in the lab and answer questions regarding the mechanisms by which a particular genetic mutation gives rise to seizures. The ultimate goal of identifying genes associated with epilepsy is to develop targeted therapies for a particular gene.[3] An even more exciting prospect of understanding the genes associated with epilepsy is the prospect of targeting the genes to potentially stop the onset of seizures before it even begins! Understanding the genetic mechanisms of epilepsy is helped by continued advances in genetic technologies, sophisticated ways to store and analyze huge datasets, and the capability to perform experiments in animals and translate findings to the human condition, thus setting the scene for precision medicine in genetic epilepsy.[4]

CURE Epilepsy’s Epilepsy Genetics Initiative (EGI) was formed in 2015 and was instrumental in creating a centralized database that holds the genetic (whole exome sequence) data of people with epilepsy. Whole exome sequencing is a way to analyze a person’s unique DNA fingerprint pattern. By analyzing and re-analyzing genetic data as techniques advance, EGI aimed to advance our understanding of the genetic causes of epilepsy so that clinicians could better and more effectively diagnose, treat, and even prevent genetic epilepsies. Thanks to GI, new genes underlying epilepsy have been found; re-analysis of patient genetic materials has led to new diagnoses for those with genetic epilepsy. Additionally, there have been benefits to the epilepsy community as well. EGI is a community resource, and the whole exome data within the database is available to the research community. All the genetic data are de-identified; hence, there is no way for information to be linked back to a patient or the patient’s family.

In addition to the formation of a centralized database, CURE Epilepsy is also intently focused on identifying and funding cutting-edge research in epilepsy curing the epilepsies. This CURE Epilepsy Discovery article will also outline the work of three CURE Epilepsy grants awardees: Dr. Heather Mefford, her mentee Dr. Gemma Carvill, and Dr. Carvill’s mentee Dr. Jeff Calhoun. By funding these outstanding researchers investigating mechanisms underlying genetic epilepsies, CURE Epilepsy is actively supporting the development of the future generation of epilepsy researchers and scientists.

Dr. Heather Mefford is currently at St. Jude Children’s Hospital and received a CURE Epilepsy Award in 2019. As part of this grant, she investigated the causes of Developmental and Epileptic Encephalopathies (DEE). DEE are severe, early-onset epilepsy disorders that are associated with developmental delay and seizures that are resistant to treatment. A specific genetic cause can be correctly identified in about half of the cases of DEE, and this identification can be associated with a correct diagnosis and a favorable prognosis (course of the disease). Also, a proper diagnosis can help the clinician connect the family to appropriate support groups as well. However, about half of those with DEE are not accurately diagnosed, even with state-of-the-art genetic testing. Work done by Dr. Mefford’s team looked for a different cause in those with DEE that are not diagnosed. Her team looked at abnormal methylation – a type of chemical modification in the DNA structure – in individuals with DEE that did not have a diagnosis or cause. Methylation is considered an “epigenetic” modification – these modifications are not hardwired into one’s DNA, but turn genes “on” and “off.” [5]

Work done by Dr. Mefford’s team has led to the development of “methylation signature” analysis by which methylation patterns of individuals with DEE without a known diagnosis can be studied. Methylation patterns have been studied for other disorders, but not comprehensively for epilepsy. More work is needed to understand the precise methylation signature in DEE; however, the goal is that one day, by diagnosing methylation patterns, we will be able to improve the diagnosis of those with DEE. An accurate diagnosis could also improve the prognosis, and clinicians will be able to accurately offer genetic counseling services to patients and families. There is also the hope of being able to provide targeted precision therapies for these specific methylation patterns.

In addition to recognizing methylation patterns, Dr. Mefford’s team has also been instrumental in characterizing de novo mutations in a gene called PPP3CA and the role of these mutations in causing epilepsy. Since mutations in the PPP3CA gene are very rare, the scientists working on this gene pooled data from different sources including CURE Epilepsy’s EGI. By collecting and analyzing data in this way, Dr. Mefford and her collaborators were able to show that mutations in the PPP3CA gene were a lead factor in the development of specific childhood-onset epilepsy. Dr. Mefford and her collaborators were also able to understand how mutations in the PPP3CA gene cause epilepsy. This gene is responsible for the production of a protein in the brain known as calcineurin; this substance is responsible for key functions in the brain, including proper signaling between neurons. Mutations in PPP3CA interfere with the ability of calcineurin in electrical transmission in the brain leading to neurodevelopmental disorders and epilepsy.[6] Hence, Dr. Mefford’s work funded and supported by CURE Epilepsy is laying the foundation for the study of epigenetics, particularly methylation, in DEE.[7]

In addition to her work as a physician caring for pediatric patients living with severe epilepsy syndromes, and her work as an epilepsy genetics researcher (described above), Dr. Mefford is also passionate about supporting the next generation of epilepsy scientists. One of her trainees, Dr. Gemma Carvill is an independent epilepsy researcher and leads her research program at Northwestern University. Dr. Carvill received CURE Epilepsy’s Taking Flight Award in 2015. The Taking Flight Award was developed to foster and develop the careers of young epilepsy investigators by allowing them to develop a research focus independent of their mentor(s). The Taking Flight Award came at an opportune time in Dr. Carvill’s career and was instrumental in directing her scientific interests in the field of epilepsy genetics.

Dr. Carvill investigated the genetic causes of the most severe forms of epilepsy known as epileptic encephalopathy. Childhood epileptic encephalopathies are a group of epilepsy disorders that are profoundly treatment-resistant; children with this condition also have severe cognitive and neurological deficits.[8,9] Specifically, she was interested in exploring the epigenomic causes of epileptic encephalopathy, i.e., studying genes that turn the activity of other genes “on” or “off”. By using a new genome-editing technology called CRISPR-Cas9 to introduce mutations in a class of genes known as “chromatin remodelers”, she was able to study the mechanisms by which these genes cause seizures.

To study the epigenomic causes of epilepsy, she studied de novo mutations in the CUX2 gene. In an international study done with Dr. Gaetan Lesca of the Lyon University Hospital, Dr. Carvill found mutations in the CUX2 gene in nine patients who started having seizures early in life, had treatment-resistant epilepsy, and severe developmental delay. Since mutations such as the one in the CUX2 gene are rare, several research teams must come together to provide statistical rigor. By identifying mutations in the CUX2 gene in epileptic encephalopathy, this gene can potentially be targeted to develop therapies.[10]

Another work done by Dr. Carvill and her team looked at another epilepsy-associated gene called SZT2. Earlier studies have shown an association between mutations in the SZT2 gene and some neurodevelopmental disorders,[11] but the full extent of the impact of mutations in this gene and its link to epilepsy was not yet known. It is also known that the SZT2 gene plays a critical role in the mammalian target of rapamycin complex 1 (mTORC1) signaling pathway which is essential in cell growth and proliferation. By using state-of-the-art genetic technologies, Dr. Carvill’s team determined that mutations in the SZT2 gene were likely pathogenic and that the mutation is more prevalent in individuals of Ashkenazi Jewish ancestry. The direct implication of these findings is the knowledge that this gene should be included in prenatal gene panels. Given that the SZT2 gene interacts with the mTORC1 pathway, and since the mTORC1 pathway is implicated in other neurodevelopmental diseases as well, there are also implications for potential treatment strategies involving the mtORC1 signaling pathway.[12]

Since receiving the Taking Flight Award, Dr. Carvill has been awarded other accolades also; notably the prestigious Innovator’s Award from the NIH. As part of this award, she will continue her work on genetic epilepsies, specifically exploring if cell-free DNA (cfDNA) could be used as a non-invasive avenue for epilepsy diagnosis and perhaps as a biomarker.[13] At Northwestern University, she too is mentoring a Taking Flight grantee, Dr. Jeffrey Calhoun.

Carrying on the tradition, Dr. Jeffrey Calhoun received the Taking Flight Award in 2022 and his research will look at genetic variants that are linked to the risk for epilepsy. He is developing methods to determine which genetic variants near SCN1A, a gene implicated in epilepsy, alter SCN1A gene expression. This technique eventually could also be used to study variants that impact other genes associated with epilepsy. By understanding the pattern of gene expression and the variants that may cause variable expression, Dr. Calhoun’s work aims to impact the diagnosis and care of those with genetic epilepsies. 

Hence, the work of Drs. Mefford, Carvill, and Calhoun together aim to develop new technologies to better understand genetic epilepsies, which many times, can be catastrophic. In addition to funding Dr. Mefford and her mentees, CURE Epilepsy is making an incredible impact on rare epilepsies, having inaugurated the Rare Epilepsy Partnership Award this year. With this partnership award providing funding for the rare and devasting epilepsies, we can not only provide hope but more understanding that will one day be translated into a cure.

Literature Cited:

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2. Steinlein OK. Genetics and epilepsy Dialogues Clin Neurosci. 2008;10:29-38.
3. Szepetowski P. Genetics of human epilepsies: Continuing progress Presse Med. 2018 Mar;47:218-226.
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10. Chatron N, Møller RS, Champaigne NL, Schneider AL, Kuechler A, Labalme A, et al. The epilepsy phenotypic spectrum associated with a recurrent CUX2 variant Ann Neurol. 2018 May;83:926-934.
11. Kariminejad A, Yazdan H, Rahimian E, Kalhor Z, Fattahi Z, Zonooz MF, et al. SZT2 mutation in a boy with intellectual disability, seizures and autistic features European Journal of Medical Genetics. 2019 2019/09/01/;62:103556.
12. Calhoun JD, Aziz MC, Happ HC, Gunti J, Gleason C, Mohamed N, et al. mTORC1 functional assay reveals SZT2 loss-of-function variants and a founder in-frame deletion Brain. 2022 Jun 30;145:1939-1948.
13. Carvill GL. Cell-free DNA sequencing approaches to define the genetic etiology of unexplained epilepsy. Accessed April 9, 2023.