Precision Medicine In Epilepsy
Precision medicine
precision medicine, defined as “treatments targeted to the needs of individual patients on the basis of genetic, biomarker, phenotypic, or psychosocial characteristics, aims to modify each individual’s disease course. In epilepsy ,efforts to date in precision medicine have primarily focused on targeting genetic causativemechanisms. 2 Success in the treatment of neuromuscular conditions3 has allowed clinicians to consider the possibility of a seismic shift in outcomes in epilepsy. However, to date, precision medicine for epilepsy has been limited to a small subset of people with monogenic disease,2 and robust evidence of efficacy is currently not available. [16,17]
Within the last 5 years, large-scale sequencing efforts have substantially contributed to our understanding of the genetic architecture of early-life epilepsies, identifying heterozygous, de novo pathogenic variants in over 30% of patients with EOEE. Conversely, copy number variants (CNVs), defined as deletions or duplications of DNA greater than 1 kb in size, have been shown to be a rare cause of early life epilepsies; approximately 3–5% of patients with epileptic and developmental encephalopathy have an explanatory pathogenic CNV. Because the majority of recent scientific progress has been made in monogenic causes of early onset epilepsies, we will focus our review on single gene causes. The early-life epilepsies are highly genetically heterogeneous, and no single causative gene has been identified in more than 1–2% of patients Additionally, genotype-phenotype correlations are often not possible in most genetic epilepsies, with patients carrying the same pathogenic variant presenting with vastly different clinical features, including age of onset, seizure severity, and developmental outcome. Despite high genetic heterogeneity, studies have highlighted important biological pathways, identifying causative variants in genes encoding voltage- and ligand gated ion channels and proteins involved in synaptic transmission.
Neuronal Ion Channels
Approximately 25% of all epilepsy-associated genes encode neuronal ion channels, making this class of genes the most important recognized genetic cause of epilepsy. The most well-recognized genetic epilepsy, Dravet syndrome, is caused by pathogenic de novo variants in SCN1A, encoding the voltage-gated sodium channel Nav1. 1. Although Dravet syndrome is the most common genetic epilepsy with an incidence of 1: 22,000 , variants in genes encoding other voltage gated sodium channels, including SCN2A and SCN8A, are also relatively common causes of severe early-life epilepsy. Pathogenic variants in SCN2A in particular are among the most commonly identified causes via diagnostic genetic testing. Genes encoding voltage-gated potassium channels, including KCNQ2, KCNA2, and KCNB1, have also been implicated in early-onset epilepsies , with pathogenic de novo variants in KCNQ2 explaining up to 80% of patients with neonatal-onset epileptic encephalopathy in some research cohorts. The phenotypic spectrum of CACNA1A-related disorders, encoding the voltage-gated calcium channel Cav2. 1, initially associated with episodic ataxia and spino cerebellar ataxia, is also expanding to include EOEE and LennoxGastaut syndrome. [22,23,24]
In addition to voltage-gated ion channels, ligand-gated ion channels also play an important role in the underlying etiology of childhood-onset epilepsies. In particular, disease-causing variants in genes for N-methyl-D-aspartate receptor (NMDA) and gamma-amino butyric acid (GABA) receptor subunits are emerging as major classes of genes. NMDA receptors are important for transmission of the main excitatory neurotransmitter, glutamate, while GABA receptors bind the main inhibitory neurotransmitter, GABA. Pathogenic variants in genes encoding NMDA receptor subunits cause a spectrum of neurodevelopmental disorders, including epilepsies within the epilepsy aphasia spectrum (GRIN2A) and severe early-onset epileptic encephalopathy (GRIN1, GRIN2B, GRIN2D). Additionally, genes encoding GABAA-receptor subunits, including GABRA1, GABRG2, and GABRB3, have been identified in patients with a spectrum of childhood onset epilepsies, spanning epileptic encephalopathy to milder familial epilepsy syndromes.
Synaptic Transmission
While variants in genes encoding ion channel subunits have long been recognized as contributing to human epilepsies, variants in genes encoding components of the synaptic transmission apparatus have only recently been recognized as playing an important role in the etiology of early-life epilepsies. One study estimates that approximately 75% of pathogenic variants in patients with epileptic encephalopathy disrupt proteins involved in synaptic transmission. STXBP1 and STX1B both encode components of the SNAP (soluble NSF attachment protein) Receptor (SNARE) complex, the molecular machinery that mediates fusion of synaptic vesicles with the plasma membrane of the presynapse.
STXBP1 haploinsufficiency was initially identified in patients with severe early-onset epileptic encephalopathy including Ohtahara syndrome and West syndrome , although the phenotypic spectrum has now expanded to include developmental delay and neurological features without epilepsy. Variants in STX1B have been associated with a fever related epilepsy beginning early in life, often associated with ataxia, intellectual disability, and autism. Defects of synaptic vesicle recycling after neurotransmitter release are also important in the etiology of early-onset epilepsies. Pathogenic variants in DNM1, which encodes the dynamic 1 protein, a molecular scissors which removes fused synaptic vesicles from the plasma membrane, are found in up to 2% of patients with West syndrome and/or Lennox-Gastaut syndrome [45]. Furthermore, PPP3CA, encoding the catalytic subunit of calcineurin responsible for dynamic 1 phosphorylation, has also recently been identified as a cause of childhood-onset epileptic and developmental encephalopathy.
Precision Genetics for Precision Medicine
Molecular genetics research in epilepsy began more than 20 years ago and has entered a phase of rapid progress. This suggests that in the near future, at least some of the important genetic risk factors contributing to epilepsy will be identified in a substantial proportion of individuals with non-acquired epilepsy. Analyses of the genes implicated to date further indicate that genetically resolved epilepsies will eventually be grouped into larger sets that share common underlying biological causes or pathways. Findings from traditional heritability studies and more recent genomic heritability analysis unequivocally show the important role of genetics in epilepsy risk. Before the development of next-generation sequencing, both linkage analyses and targeted candidate gene studies identified a number of epilepsy genes. Although these discoveries represented a substantial advance and illuminated novel aspects of disease pathophysiology, collectively these genes underlie epilepsy in only a small proportion of individuals with the disorder.
The role of common variation in epilepsy has also been assessed, both with candidate genes and comprehensive genome-wide association studies (GWAS) with generally limited findings. In parallel, chromosome microarrays have been used to identify copy-number variants that confer substantial risk of epilepsy. Although each copy number variant confers significant risk, none is sufficient to cause epilepsy alone, and all variants are associated with several neuropsychiatric diseases. Collectively, these findings led researchers to focus on rare variants in epilepsy precisely when developments in next-generation sequencing facilitated the comprehensive interrogation of genomes.
The most common application of next-generation sequencing is to investigate the “exome,” or the set of nearly all protein-coding regions of the genome. Trio sequencing, in particular, in which the genomes of the individual with epilepsy and both parents are sequenced, is a successful method to identify new risk factors for the epileptic encephalopathy (panel), as well as for other neuropsychiatric diseases, including intellectual disability and autism spectrum disorders. In the EEs alone, trio-based analyses have led to the identification of ALG13, GABRB3, DNM1, HCN1, GRIN2A, GABRA, GNAO1, KCNT1, SCN2A, SCN8A, and SLC35A2 as genes associated with epilepsy. Interestingly, and not surprisingly, many of the proteins encoded by these genes are involved in synaptic transmission. The characterization of the specific effects of mutations in these genes will help to resolve the precise biological pathways within the synaptic transmission that are disrupted in epilepsy. [35,36]
Post-zygotic (somatic) de novo mutations (panel) that are present in only a subset of cells have also been identified as the cause of malformation syndromes associated with severe epilepsy. Recent examples include somatic mutations in AKT3, MTOR and PICK3CA as the cause of hemimegalencephaly and intractable seizures, and somatic mutations in DCX, LIS1, FLNA, and TUBB2B as the cause of double cortex syndrome, periventricular nodular heterotopia, and pachygyria. [37] To date, progress has been modest in understanding less severe forms of epilepsy, almost certainly owing to a combination of very high locus and allelic heterogeneity and the possibility that combined effects of variants in multiple genes underlie susceptibility. We anticipate that larger sample sizes will soon be available to facilitate discovery in these more genetically complex epilepsies. These epilepsies might also depend on more subtle regulatory variants, requiring application of genomic and transcriptomic approaches, an emerging area of focus in common diseases including epilepsy. We note that epilepsies that occur in response to precipitating factors such as traumatic brain injury or brain tumors, although having some genetic component, will probably be less tractable targets for precision medicine than epilepsies whose etiology is largely genetic.
Despite the progress towards the identification of epilepsy risk genes, precision medicine depends on the identification of mutations that contribute to disease in individual patients. This represents a distinct and more difficult challenge than the simple determination that a gene is involved in risk of epilepsy at the population level. The development of methods to quantitatively assess the degree of confidence that specific mutations contribute to disease in particular individuals is therefore a priority in epilepsy precision medicine. One recently developed approach to help pinpoint pathogenic mutations involves comparison of the patterns of genetic variation, including both types of mutations and their frequencies, between the general population and the population of individuals with disease.
These analyses indicate that disease genes, particularly genes associated with neuropsychiatric disorders, tend to have less common functional variation in the general population than expected given the overall predicted mutability of the genes. Indeed, bioinformatics signatures that integrate such “gene level” scores with established variant level scores have been shown to be predictive of causative mutations in the genomes of individuals with severe early-onset diseases. A key focus of emerging efforts in epilepsy precision medicine will be to develop new statistical genetic approaches to expand these research areas, including analyses in diverse ethnic groups, and analyses of mutation patterns in non-coding genomic regions. In view of the need for expanded sample sizes, both for gene discovery and to facilitate accurate interpretation of individual genomes, genetic data generated in different locations must be integrated as much as possible. Importantly, data are being collected in commercial genetic testing laboratories that do exam sequencing on a fee-for-service basis, but these data are largely unavailable for research at this time.
To make more effective use of these data, the epilepsy community has come together to establish the Epilepsy Genetics Initiative (EGI) to integrate clinical data collected in medical centers and to allow the integration of clinical data with research data.
EGI has created a database to house the clinically sequenced exams (and, in due course, sequenced genomes) and phenotypic data of individuals with epilepsy, one unique purpose of which is to allow on-going iterative reassessment of unsolved cases. Thus, EGI is a resource that brings together people with epilepsy, clinicians, and researchers in a mutually beneficial effort to advance precision diagnostics and epilepsy research. Central to these discussions is the perspective of families living with epilepsy (TJD-S, unpublished). Taken together, developments in gene discovery, bioinformatic prioritization of putative pathogenic mutations, and large-scale genetic data integration suggest that the genetic basis for precision medicine in epilepsy is now within reach. As an illustration, the list of known epilepsy genes that can form the initial basis for epilepsy precision medicine is growing.
Precision medicine in the epilepsies also has an equally important role in facilitating avoidance of adverse reactions as in maximizing efficacy, as illustrated by a number of recent examples. In some cases, improved diagnostics will enable avoidance of adverse reactions, as is the case for patients with epilepsy due to POLG1 mutations who might develop fatal hepatic failure when treated with valproate. In other cases the risk factors for a severe adverse reaction will be independent of factors responsible for the disease; for example, the HLA-B*15:02 allele is highly predictive of carbamazepine-induced Stevens-Johnson syndrome, a severe hypersensitivity reaction, in patients of Asian origin.
