Real-life survey of pitfalls and successes of precision medicine in genetic epilepsies

Precision medicine in epilepsy: Clinicians' perspectives from an international qualitative study

OBJECTIVE

Precision medicine (PM) is gaining increasing importance in the treatment of rare genetic epilepsies. However, its availability and implementation in clinical practice remain limited. This study explores the barriers and facilitators influencing the implementation of PM for people with epilepsy (PWE).

METHODS

Semistructured interviews were conducted with clinicians involved in epilepsy care for PWE across various global regions. Participants were purposefully selected based on geographical distribution and World Bank income classification. Framework analysis was used to identify key themes.

RESULTS

Sixteen clinicians from six different continents were interviewed. Five key themes emerged. The implementation of PM depends on (1) the personal perspective and experience of health care providers; (2) the attitude of PWE and their caregivers toward PM, and their interaction with clinicians; (3) continuous education of health care providers, formation of expert teams, and generation of robust evidence on PM; (4) multilevel collaboration including patient advocacy groups; and (5) a clear, consistent organizational approach and the development and implementation of standardized guidelines.

SIGNIFICANCE

Clinicians consider PM as transformative for the care for PWE and expect it to redefine standard practice in the near future. Insufficient knowledge is the primary barrier to PM implementation, irrespective of socioeconomic context, highlighting the need for its integration into basic medical training and residency programs. To address inequities, integrated care pathways and standardized guidelines for genetic testing and PM, and the establishment of local PM-focused expert teams are essential to support clinicians in making informed PM decisions.

Monogenic Epilepsies in Adult Epilepsy Clinics and Gene-Driven Approaches to Treatment

PURPOSE OF REVIEW

Genetic factors play an important contribution to the aetiology of epilepsy and may have implications for management. Whilst the study of monogenic epilepsies has predominantly centred around children, there is a critical need to understand the burden of monogenic epilepsies in adults. This understanding is essential to steer the application of genetic testing and to facilitate access to gene-driven therapies in adults with epilepsy.

RECENT FINDINGS

The yield of diagnostic genetic testing in adults with epilepsy and neurodevelopmental disorders is similar to that in children (ranging from 23-50%). Distinct causal genes underlie the most common monogenic epilepsies identified in adulthood compared to childhood, although SCN1A is the most commonly implicated gene across both populations. Genetic diagnoses made in adults with epilepsy frequently have direct implications for clinical management. However, very few gene-driven therapies are supported by evidence from formal studies. Genetic testing should be considered in adults with unexplained epilepsy and may have important implications for management, including the potential for gene-driven therapies. However, further work is needed to understand the outcomes of gene-driven therapies in adults with epilepsy.

National survey on the prevalence of single-gene aetiologies for genetic developmental and epileptic encephalopathies in Italy

BACKGROUND

We aimed to estimate real-world evidence of the prevalence rate of genetic developmental and epileptic encephalopathies (DEEs) in the Italian population over a 11-year period.

METHODS

Fifteen paediatric and adult tertiary Italian epilepsy centres participated in a survey related to 98 genes included in the molecular diagnostic workflows of most centres. We included patients with a clinical diagnosis of DEE, caused by a pathogenic or likely pathogenic variant in one of the selected genes, with a molecular diagnosis established between 2012 and 2022. These data were used as a proxy to estimate the prevalence rate of DEEs.

RESULTS

We included 1568 unique patients and found a mean incidence proportion of 2.6 patients for 100.000 inhabitants (SD=1.13) with consistent values across most Italian regions. The number of molecular diagnoses showed a continuing positive trend, resulting in more than a 10-fold increase between 2012 and 2022. The mean age at molecular diagnosis was 11.2 years (range 0-75). Pathogenic or likely pathogenic variants in genes with an autosomal dominant inheritance pattern occurred in 77% (n=1207) patients; 17% (n=271) in X-linked genes and 6% (n=90) in genes with autosomal recessive inheritance. The most frequently reported genes in the survey were SCN1A (16%), followed by KCNQ2 (5.6%) and SCN2A (5%).

CONCLUSION

Our study provides a large dataset of patients with monogenic DEE, from a European country. This is essential for informing decision-makers in drug development on the appropriateness of initiatives aimed at developing precision medicine therapies and is instrumental in implementing disease-specific registries and natural history studies.

Epilepsy genetics in the paediatric population of the Eastern Anatolia region of Turkey

This study investigates the genetic causes of epilepsy in 166 paediatric patients under the age of 16 from the East Anatolian region of Turkey, who were treated at Erzurum City Hospital between 2018 and 2023. Patients with early-onset seizures, a family history of epilepsy or intellectual disability was selected for genetic analysis using a next-generation sequencing (NGS) gene panel targeting 449 genes associated with epilepsy and epileptic encephalopathy. The analysis revealed that pathogenic or probable pathogenic mutations were present in 14.8% (32 patients), highlighting the significant role of genetic factors in the aetiology of epilepsy in this population. In addition, 30.6% (66 patients) carried variants of uncertain significance (VUS), which, although not classified as pathogenic, have potential clinical relevance. Many epilepsy-related genes follow an autosomal dominant inheritance pattern, meaning that VUSs may gain pathogenic significance as more data and global studies accumulate, emphasising the evolving nature of genetic research. In addition to genetic factors, other aetiological causes such as perinatal insults (15.3%) and infections (7.9%) were identified, highlighting the multifactorial origin of epilepsy. While pathogenic mutations currently serve as important diagnostic and therapeutic markers, the role of VUS should not be underestimated. Genetic testing has proven to be essential for understanding the complex causes of epilepsy, providing opportunities for personalised treatment and genetic counselling. This study highlights the importance of genetic testing in regions such as Eastern Anatolia, where both environmental and genetic factors may influence the prevalence of epilepsy. As genetic databases expand, it is likely that the understanding of VUS will evolve, improving the clinical management of epilepsy through more targeted therapies and improved outcomes.

Developmental and epileptic encephalopathies

Developmental and epileptic encephalopathies, the most severe group of epilepsies, are characterized by seizures and frequent epileptiform activity associated with developmental slowing or regression. Onset typically occurs in infancy or childhood and includes many well-defined epilepsy syndromes. Patients have wide-ranging comorbidities including intellectual disability, psychiatric features, such as autism spectrum disorder and behavioural problems, movement and musculoskeletal disorders, gastrointestinal and sleep problems, together with an increased mortality rate. Problems change with age and patients require substantial support throughout life, placing a high psychosocial burden on parents, carers and the community. In many patients, the aetiology can be identified, and a genetic cause is found in >50% of patients using next-generation sequencing technologies. More than 900 genes have been identified as monogenic causes of developmental and epileptic encephalopathies and many cell components and processes have been implicated in their pathophysiology, including ion channels and transporters, synaptic proteins, cell signalling and metabolism and epigenetic regulation. Polygenic risk score analyses have shown that common variants also contribute to phenotypic variability. Holistic management, which encompasses antiseizure therapies and care for multimorbidities, is determined both by epilepsy syndrome and aetiology. Identification of the underlying aetiology enables the development of precision medicines to improve the long-term outcome of patients with these devastating diseases.

The 2017 and 2022 ILAE epilepsy classification systems identify needs and opportunities in care: A paediatric hospital-based study

OBJECTIVES

There is a paucity of studies reporting the epilepsy spectrum using the 2017 and 2022 ILAE classification systems in everyday clinical practice. To identify gaps and opportunities in care we evaluated a hospital-based cohort applying these epilepsy classification systems, including aetiology and co-morbidity, and the utility of molecular genetic diagnosis to identify available precision therapies.

METHODS

Cross sectional retrospective study of all children with epilepsy (≤16 years) attending University Hospital Galway (2017-2022). Data collection and analysis of each case was standardised to ensure a systematic approach and application of the recent ILAE categorisation and terminology (2017 and 2022). Ethics approval was obtained.

RESULTS

Among 356 children, epilepsy was classified as focal (46.1 %), generalised (38.8 %), combined (6.2 %), and unknown (9 %). Epilepsy syndrome was determined in 145/356 (40.7 %), comprising 24 different syndromes, most commonly SeLECTS (9 %), CAE (7 %), JAE (6.2 %) and IESS (5.9 %). New aetiology-specific syndromes were identified (e.g. CDKL5-DEE). Molecular diagnosis was confirmed in 19.9 % (n = 71) which encompassed monogenic (13.8 %) and chromosomopathy/CNV (6.2 %). There was an additional 35.7 % (n = 127) of patients who had a presumed genetic aetiology of epilepsy. Remaining aetiology included structural (18.8 %, n = 67), infectious (2 %, n = 7), metabolic (1.7 %, n = 6) and unknown (30.3 %, n = 108). Encephalopathy categorisation was determined in 182 patients (DE in 38.8 %; DEE in a further 11.8 %) associated with a range of co-morbidities categorised as global delay (29.2 %, n = 104), severe neurological impairment (16.3 %, n = 58), and ASD (14.6 %, n = 52). Molecular-based "precision therapy" was deemed available in 21/356 (5.9 %) patients, with "molecular precision" approach utilised in 13/356 (3.7 %), and some benefit noted in 6/356 (1.7 %) of overall cohort or 6/71 (8.5 %) of the molecular cohort.

CONCLUSION

Applying the latest ILAE epilepsy classification systems allow comparison across settings and identifies a major neuro-developmental co-morbidity rate and a large genetic aetiology. We identified very few meaningful molecular-based disease modifying "precision therapies". There is a monumental gap between aetiological identification, and impact of meaningful therapies, thus the new 2017/2022 classification clearly identifies the major challenges in the provision of routine epilepsy care.

Genetic variant interpretation for the neurologist - A pragmatic approach in the next-generation sequencing era in childhood epilepsy

Genetic advances over the past decade have enhanced our understanding of the genetic landscape of childhood epilepsy. However a major challenge for clinicians ha been understanding the rationale and systematic approach towards interpretation of the clinical significance of variant(s) detected in their patients. As the clinical paradigm evolves from gene panels to whole exome or whole genome testing including rapid genome sequencing, the number of patients tested and variants identified per patient will only increase. Each step in the process of variant interpretation has limitations and there is no single criterion which enables the clinician to draw reliable conclusions on a causal relationship between the variant and disease without robust clinical phenotyping. Although many automated online analysis software tools are available, these carry a risk of misinterpretation. This guideline provides a pragmatic, real-world approach to variant interpretation for the child neurologist. The focus will be on ascertaining aspects such as variant frequency, subtype, inheritance pattern, structural and functional consequence with regard to genotype-phenotype correlations, while refraining from mere interpretation of the classification provided in a genetic test report. It will not replace the expert advice of colleagues in clinical genetics, however as genomic investigations become a first-line test for epilepsy, it is vital that neurologists and epileptologists are equipped to navigate this landscape.

Guidelines for Specialized Epilepsy Centers: Executive Summary of the Report of the National Association of Epilepsy Centers Guideline Panel

The National Association of Epilepsy Centers first published the guidelines for epilepsy centers in 1990, which were last updated in 2010. Since that update, epilepsy care and the science of guideline development have advanced significantly, including the importance of incorporating a diversity of stakeholder perspectives such as those of patients and their caregivers. Currently, despite extensive published data examining the efficacy of treatments and diagnostic testing for epilepsy, there remain significant gaps in data identifying the essential services needed for a comprehensive epilepsy center and the optimal manner for their delivery. The trustworthy consensus-based statements (TCBS) process produces unbiased, scientifically valid guidelines through a transparent process that incorporates available evidence and expert opinion. A systematic literature search returned 5937 relevant studies from which 197 articles were retained for data extraction. A panel of 41 stakeholders with diverse expertise evaluated this evidence and drafted recommendations following the TCBS process. The panel reached consensus on 52 recommendations covering services provided by specialized epilepsy centers in both the inpatient and outpatient settings in major topic areas including epilepsy monitoring unit care, surgery, neuroimaging, neuropsychology, genetics, and outpatient care. Recommendations were informed by the evidence review and reflect the consensus of a broad panel of expert opinions.

Validation of targeted next-generation sequencing panels in a cohort of Polish patients with epilepsy: assessing variable performance across clinical endophenotypes and uncovering novel genetic variants

Introduction

Targeted Next-Generation Sequencing Panels (TNGSP) have become a standard in global clinical practice. Instead of questioning the necessity of next-generation sequencing in epilepsy patients, contemporary large-scale research focuses on factors such as the size of TNGSP, the comparative advantages of exome or genome-wide sequencing over TNGSP, and the impact of clinical, electrophysiological, and demographic variables on genetic test performance. This study aims to elucidate the demographic and clinical factors influencing the performance of TNGSP in 138 Polish patients with epilepsy, recognizing the pivotal role of genetic testing in guiding patient management and therapy.

Methods

A retrospective analysis was conducted on patients from a genetic clinic in Poznań, Poland, who underwent commercial gene panel studies at Invitae Corporation (USA) between 2020 and 2022. Patient groups were defined based on the age of onset of the first epileptic seizures, seizure type, gender, fever dependence of seizures, presence of intellectual disability or developmental delay, abnormalities in MRI, and the presence of dysmorphic features or congenital malformations. Seizure classification followed the 2017 ILAE criteria.

Results

Among the 138 patients, 30 (21.7%) exhibited a pathogenic or likely pathogenic variant, with a distribution of 20.7% in males and 22.5% in females. Diagnostic performance correlated with the patient's age at the onset of the first seizure and the type of seizure. Predominant variants were identified in the SCN1A, PRRT2, CDKL5, DEPDC5, TSC2, and SLC2A1 genes. Additionally, 12 genes (CACNA1A, SCN2A, GRIN2A, KCNQ2, CHD2, DYNC1H1, NEXMIF, SCN1B, DDX3X, EEF1A2, NPRL3, UBE3A) exhibited single instances of damage. Notably, novel variants were discovered in DEPDC5, SCN1A, TSC2, CDKL5, NPRL3, DYNC1H1, CHD2, and DDX3X.

Discussion

Identified variants were present in genes previously recognized in both European and non-European populations. A thorough examination of Variants of Uncertain Significance (VUSs), specifically focusing on gene copy number changes, may unveil more extensive chromosomal aberrations. The relatively frequent occurrence of pathological variants in X chromosome-linked genes in girls warrants further investigation, challenging the prevailing notion of male predominance in X-linked epilepsy.

Epilepsies

Recent advances in genetic diagnosis have revealed the underlying etiology of many epilepsies and have identified pathogenic, causative variants in numerous ion and ligand-gated channel genes. This chapter describes the clinical presentations of epilepsy associated with different channelopathies including classic electroclinical syndromes and emerging gene-specific phenotypes. Also discussed are the archetypal epilepsy channelopathy, SCN1A-Dravet syndrome, considering the expanding phenotype. Clinical presentations where a channelopathy is suspected, such as sleep-related hypermotor epilepsy and epilepsy in association with movement disorders, are reviewed. Channelopathies pose an intriguing problem for the development of gene therapies. Design of targeted therapies requires physiologic insights into the often multifaceted impact of a pathogenic variant, coupled with an understanding of the phenotypic spectrum of a gene. As gene-specific novel therapies come online for the channelopathies, it is essential that clinicians are able to recognize epilepsy phenotypes likely to be due to channelopathy and institute early genetic testing in both children and adults. These findings are likely to have immediate management implications and to inform prognostic and reproductive counseling.

From diagnosis to treatment in genetic epilepsies: Implementation of precision medicine in real-world clinical practice

The implementation of whole exome sequencing (WES) has had a major impact on the diagnostic yield of genetic testing in individuals with epilepsy. The identification of a genetic etiology paves the way to precision medicine: an individualized treatment approach, based on the disease pathophysiology. The aim of this retrospective cohort study was to: (1) determine the diagnostic yield of WES in a heterogeneous cohort of individuals with epilepsy referred for genetic testing in a real-world clinical setting, (2) investigate the influence of epilepsy characteristics on the diagnostic yield, (3) determine the theoretical yield of treatment changes based on genetic diagnosis and (4) explore the barriers to implementation of precision medicine. WES was performed in 247 individuals with epilepsy, aged between 7 months and 68 years. In 34/247 (14 %) a (likely) pathogenic variant was identified. In 7/34 (21 %) of these individuals the variant was found using a HPO-based filtering. Diagnostic yield was highest for individuals with an early onset of epilepsy (39 %) or in those with a developmental and epileptic encephalopathy (34 %). Precision medicine was a theoretical possibility in 20/34 (59 %) of the individuals with a (likely) pathogenic variant but implemented in only 11/34 (32 %). The major barrier to implementation of precision treatment was the limited availability or reimbursement of a given drug. These results confirm the potential impact of genetic analysis on treatment choices, but also highlight the hurdles to the implementation of precision medicine. To optimize precision medicine in real-world practice, additional endeavors are needed: unifying definitions of precision medicine, establishment of publicly accessible databases that include data on the functional effect of gene variants, increasing availability and reimbursement of precision therapeutics, and broadening access to innovative clinical trials.

Retracted: Clinical and genetic evaluations of rare childhood epilepsies in Turkey's national cohort

Aycan Ünalp, Yiğithan Güzin, Bülent Ünay, Ayşe Tosun, Dilek Çavuşoğlu, Hande Gazeteci Tekin, Semra Hız Kurul, Ebru Arhan, Selvinaz Edizer, Gülten Öztürk, Uluç Yiş, Ünsal Yılmaz, Turkish Rare Epilepsies Study Group, Clinical and genetic evaluations of rare childhood epilepsies in Turkey's national cohort, Epileptic Disorders, 2023, (https://doi.org/10.1002/epd2.20150) The above article, published online on 16 August 2023 on Wiley Online Library (www.onlinelibrary.wiley.com), has been retracted by agreement between the authors, the Editor-in-Chief, Sándor Beniczky, and John Wiley & Sons Ltd. The authors asked for a retraction based on an experimental error which would alter the results of the study if corrected.

Genome-Based Therapeutics: Era of Precision Medicine in Genetic Epilepsies and Epileptic Encephalopathies

Introduction

The recent evolution of genomics has led to the development of targeted therapeutics, revolutionizing medical approaches. This study aimed to assess the impact of genetic testing on the current epilepsy management paradigm with a specific focus on the variability of outcomes subsequent to genetic diagnoses.

Methodology

Data were collected retrospectively from a cohort of children aged 1-18 years, diagnosed with refractory epilepsy of confirmed genetic origin. The participants received care at a quaternary care center's pediatric neurology clinic from August 2019 to June 2021. The collected information included demographic characteristics, seizure types, EEG findings, imaging abnormalities, genetic diagnoses, attempted treatments, and seizure outcomes.

Results

Among the 210 children with confirmed genetic diagnoses, 74 were included in the study. The gender distribution comprised 45 males and 29 females. Within the cohort, 68/74 exhibited single gene variations, with 23 cases associated with sodium/potassium/calcium channelopathies. Precision medicine could be applied to 25/74 cases. 17/74 children (22.97%) experienced a reduction of up to 50% in seizure frequency due to precision medicine implementation.

Conclusion

While our study indicates the significance of genetic insights in adapting treatment approaches for pediatric epilepsy, it is important to temper our conclusions. The retrospective nature of our study confines our ability to definitively gauge the extent of precision medicine's utility. Our findings suggest the potential of genetic information to enhance epilepsy management, but the true impact of precision medicine can only be established through prospective investigations.

Zebrafish as a robust preclinical platform for screening plant-derived drugs with anticonvulsant properties-a review

Traditionally, selected plant sources have been explored for medicines to treat convulsions. This continues today, especially in countries with low-income rates and poor medical systems. However, in the low-income countries, plant extracts and isolated drugs are in high demand due to their good safety profiles. Preclinical studies on animal models of seizures/epilepsy have revealed the anticonvulsant and/or antiepileptogenic properties of, at least some, herb preparations or plant metabolites. Still, there is a significant number of plants known in traditional medicine that exert anticonvulsant activity but have not been evaluated on animal models. Zebrafish is recognized as a suitable in vivo model of epilepsy research and is increasingly used as a screening platform. In this review, the results of selected preclinical studies are summarized to provide credible information for the future development of effective screening methods for plant-derived antiseizure/antiepileptic therapeutics using zebrafish models. We compared zebrafish vs. rodent data to show the translational value of the former in epilepsy research. We also surveyed caveats in methodology. Finally, we proposed a pipeline for screening new anticonvulsant plant-derived drugs in zebrafish ("from tank to bedside and back again").

Suberoylanilide Hydroxamic Acid (SAHA) Is a Driver Molecule of Neuroplasticity: Implication for Neurological Diseases

Neuroplasticity is a crucial property of the central nervous system to change its activity in response to intrinsic or extrinsic stimuli. This is mainly achieved through the promotion of changes in the epigenome. One of the epi-drivers priming this process is suberoylanilide hydroxamic acid (SAHA or Vorinostat), a pan-histone deacetylase inhibitor that modulates and promotes neuroplasticity in healthy and disease conditions. Knowledge of the specific molecular changes induced by this epidrug is an important area of neuro-epigenetics for the identification of new compounds to treat cognition impairment and/or epilepsy. In this review, we summarize the findings obtained in cellular and animal models of various brain disorders, highlighting the multiple mechanisms activated by SAHA, such as improvement of memory, learning and behavior, and correction of faulty neuronal functioning. Supporting this evidence, in vitro and in vivo data underline how SAHA positively regulates the expression of neuronal genes and microtubule dynamics, induces neurite outgrowth and spine density, and enhances synaptic transmission and potentiation. In particular, we outline studies regarding neurodevelopmental disorders with pharmaco-resistant seizures and/or severe cognitive impairment that to date lack effective drug treatments in which SAHA could ameliorate defective neuroplasticity.

What are the considerations when initiating treatment for epilepsy in children?

INTRODUCTION

There is a very wide spectrum of epilepsies and developmental and epileptic encephalopathies that affect children, from self-limited forms, not necessarily requiring treatment, to severe drug-resistant ones.

AREAS COVERED

In this perspective, the authors discuss the main factors to consider before drug prescription in children, considering the most recent clinical research, including age, seizure type, epilepsy syndrome, etiology, efficacy and safety profile, comorbidities, gender, available formulations, costs and drug coverage, and regulatory issues. The literature search was conducted through a PubMed search on antiseizure medications for patients aged 0-18, with respect to each of the aforementioned factors, and by checking the reference lists of relevant papers.

EXPERT OPINION

The most expanding field of research and innovation for clinical practice is precision medicine, which addresses the holistic treatment of genetic epilepsies and developmental and epileptic encephalopathies. It achieves this by addressing their detrimental effects on synapses, neurotransmission, and cellular signaling pathways with the double aim to treat seizures and to rescue neurodevelopmental trajectories, but also the issue of adverse events and drug resistance through pharmacogenomics.

How have the recent updated epilepsy classifications impacted on diagnosis and treatment?

INTRODUCTION

Epilepsies are a diverse group of disorders which differ regarding prognosis for seizure control and associated comorbidities. Accurate classification is critical to choose the highest yield investigations and best therapeutic options and to provide the most accurate prognoses regarding the expected degree of seizure control, possible remission, and risk of associated comorbidities to patients and their families. This article reviews the recent updates in epilepsy classification to illustrate how accurate classification impacts care for persons with epilepsy.

AREAS COVERED

The authors discuss the ILAE 2017 Classification of the Epilepsies along with the modification of the classification for neonatal seizures and epilepsies. They also discuss the ILAE position papers on Epilepsy syndromes in neonates and infants and children of variable age and the Idiopathic Generalized Epilepsies.

EXPERT OPINION

Accurate epilepsy classification allows selection of the highest yield investigations, choice of optimal therapies, and accurate prognostication of seizures (likelihood of response to antiseizure treatments and likelihood of remission with age), as well as comorbidities (likelihood, type, and severity). As we move into the era of disease modifying therapy, early accurate identification of underlying causes with timely introduction of specific treatments will be crucial to lessen the severity of epilepsy, with improved seizure control and attenuation of associated comorbidities.

Drug resistance in epilepsy

Drug resistance is estimated to affect about a third of individuals with epilepsy, but its prevalence differs in relation to the epilepsy syndrome, the cause of epilepsy, and other factors such as age of seizure onset and presence of associated neurological deficits. Although drug-resistant epilepsy is not synonymous with unresponsiveness to any drug treatment, the probability of achieving seizure freedom on a newly tried medication decreases with increasing number of previously failed treatments. After two appropriately used antiseizure medications have failed to control seizures, individuals should be referred whenever possible to a comprehensive epilepsy centre for diagnostic re-evaluation and targeted management. The feasibility of epilepsy surgery and other treatments, including those targeting the cause of epilepsy, should be considered early after diagnosis. Substantial evidence indicates that a delay in identifying an effective treatment can adversely affect ultimate outcome and carry an increased risk of cognitive disability, other comorbidities, and premature mortality. Research on mechanisms of drug resistance and novel therapeutics is progressing rapidly, and potentially improved treatments, including those targeting disease modification, are on the horizon.

Neurophysiology, Neuropsychology, and Epilepsy, in 2022: Hills We Have Climbed and Hills Ahead. Neurophysiology in epilepsy

Since the discovery of the human electroencephalogram (EEG), neurophysiology techniques have become indispensable tools in our armamentarium to localize epileptic seizures. New signal analysis techniques and the prospects of artificial intelligence and big data will offer unprecedented opportunities to further advance the field in the near future, ultimately resulting in improved quality of life for many patients with drug-resistant epilepsy. This article summarizes selected presentations from Day 1 of the two-day symposium "Neurophysiology, Neuropsychology, Epilepsy, 2022: Hills We Have Climbed and the Hills Ahead". Day 1 was dedicated to highlighting and honoring the work of Dr. Jean Gotman, a pioneer in EEG, intracranial EEG, simultaneous EEG/ functional magnetic resonance imaging, and signal analysis of epilepsy. The program focused on two main research directions of Dr. Gotman, and was dedicated to "High-frequency oscillations, a new biomarker of epilepsy" and "Probing the epileptic focus from inside and outside". All talks were presented by colleagues and former trainees of Dr. Gotman. The extended summaries provide an overview of historical and current work in the neurophysiology of epilepsy with emphasis on novel EEG biomarkers of epilepsy and source imaging and concluded with an outlook on the future of epilepsy research, and what is needed to bring the field to the next level.

Gene variant effects across sodium channelopathies predict function and guide precision therapy

Pathogenic variants in the voltage-gated sodium channel gene family lead to early onset epilepsies, neurodevelopmental disorders, skeletal muscle channelopathies, peripheral neuropathies and cardiac arrhythmias. Disease-associated variants have diverse functional effects ranging from complete loss-of-function to marked gain-of-function. Therapeutic strategy is likely to depend on functional effect. Experimental studies offer important insights into channel function but are resource intensive and only performed in a minority of cases. Given the evolutionarily conserved nature of the sodium channel genes, we investigated whether similarities in biophysical properties between different voltage-gated sodium channels can predict function and inform precision treatment across sodium channelopathies. We performed a systematic literature search identifying functionally assessed variants in any of the nine voltage-gated sodium channel genes until 28 April 2021. We included missense variants that had been electrophysiologically characterized in mammalian cells in whole-cell patch-clamp recordings. We performed an alignment of linear protein sequences of all sodium channel genes and correlated variants by their overall functional effect on biophysical properties. Of 951 identified records, 437 sodium channel-variants met our inclusion criteria and were reviewed for functional properties. Of these, 141 variants were epilepsy-associated (SCN1/2/3/8A), 79 had a neuromuscular phenotype (SCN4/9/10/11A), 149 were associated with a cardiac phenotype (SCN5/10A) and 68 (16%) were considered benign. We detected 38 missense variant pairs with an identical disease-associated variant in a different sodium channel gene. Thirty-five out of 38 of those pairs resulted in similar functional consequences, indicating up to 92% biophysical agreement between corresponding sodium channel variants (odds ratio = 11.3; 95% confidence interval = 2.8 to 66.9; P < 0.001). Pathogenic missense variants were clustered in specific functional domains, whereas population variants were significantly more frequent across non-conserved domains (odds ratio = 18.6; 95% confidence interval = 10.9-34.4; P < 0.001). Pore-loop regions were frequently associated with loss-of-function variants, whereas inactivation sites were associated with gain-of-function (odds ratio = 42.1, 95% confidence interval = 14.5-122.4; P < 0.001), whilst variants occurring in voltage-sensing regions comprised a range of gain- and loss-of-function effects. Our findings suggest that biophysical characterisation of variants in one SCN-gene can predict channel function across different SCN-genes where experimental data are not available. The collected data represent the first gain- versus loss-of-function topological map of SCN proteins indicating shared patterns of biophysical effects aiding variant analysis and guiding precision therapy. We integrated our findings into a free online webtool to facilitate functional sodium channel gene variant interpretation (http://SCN-viewer.broadinstitute.org).

Genetic Testing to Inform Epilepsy Treatment Management From an International Study of Clinical Practice

Importance

It is currently unknown how often and in which ways a genetic diagnosis given to a patient with epilepsy is associated with clinical management and outcomes.

Objective

To evaluate how genetic diagnoses in patients with epilepsy are associated with clinical management and outcomes.

Design, Setting, and Participants

This was a retrospective cross-sectional study of patients referred for multigene panel testing between March 18, 2016, and August 3, 2020, with outcomes reported between May and November 2020. The study setting included a commercial genetic testing laboratory and multicenter clinical practices. Patients with epilepsy, regardless of sociodemographic features, who received a pathogenic/likely pathogenic (P/LP) variant were included in the study. Case report forms were completed by all health care professionals.

Exposures

Genetic test results.

Main Outcomes and Measures

Clinical management changes after a genetic diagnosis (ie, 1 P/LP variant in autosomal dominant and X-linked diseases; 2 P/LP variants in autosomal recessive diseases) and subsequent patient outcomes as reported by health care professionals on case report forms.

Results

Among 418 patients, median (IQR) age at the time of testing was 4 (1-10) years, with an age range of 0 to 52 years, and 53.8% (n = 225) were female individuals. The mean (SD) time from a genetic test order to case report form completion was 595 (368) days (range, 27-1673 days). A genetic diagnosis was associated with changes in clinical management for 208 patients (49.8%) and usually (81.7% of the time) within 3 months of receiving the result. The most common clinical management changes were the addition of a new medication (78 [21.7%]), the initiation of medication (51 [14.2%]), the referral of a patient to a specialist (48 [13.4%]), vigilance for subclinical or extraneurological disease features (46 [12.8%]), and the cessation of a medication (42 [11.7%]). Among 167 patients with follow-up clinical information available (mean [SD] time, 584 [365] days), 125 (74.9%) reported positive outcomes, 108 (64.7%) reported reduction or elimination of seizures, 37 (22.2%) had decreases in the severity of other clinical signs, and 11 (6.6%) had reduced medication adverse effects. A few patients reported worsening of outcomes, including a decline in their condition (20 [12.0%]), increased seizure frequency (6 [3.6%]), and adverse medication effects (3 [1.8%]). No clinical management changes were reported for 178 patients (42.6%).

Conclusions and Relevance

Results of this cross-sectional study suggest that genetic testing of individuals with epilepsy may be materially associated with clinical decision-making and improved patient outcomes.

Developmental and epileptic encephalopathies - therapeutic consequences of genetic testing

Developmental and epileptic encephalopathies comprise a heterogeneous group of monogenic neurodevelopmental disorders characterized by early-onset seizures, marked epileptic activity and abnormal neurocognitive development. The identification of an increasing number of underlying genetic alterations and their pathophysiological roles in cellular signaling drives the way toward novel precision therapies. The implementation of novel treatments that target the underlying mechanisms gives hope for disease modification that will improve not only the seizure burden but also the neurodevelopmental outcome of affected children. So far, beneficial effects are mostly reported in individual trials and small numbers of patients. There is a need for international collaborative studies to define the natural history and relevant outcome measures and to test novel pharmacological approaches.

Genetic testing in adults with developmental and epileptic encephalopathy - what do we know?

Knowledge of underlying genetic causes of developmental and epileptic encephalopathies (DEE) in adults is still limited when compared to the routine diagnostic approach in similarly affected children. A well-documented longitudinal study of adults with DEE is of utmost importance to understand the natural history of the respective entity. This information is of great value especially for genetic counselling of newly diagnosed children with identical genetic diagnoses and may impact treatment and management of affected individuals. In our meta-analysis we provide an overview of the most recurrent genetic findings across an adult DEE cohort (n = 1 , 020 ). The gene mostly associated with a pathogenic or likely pathogenic variant in adult DEE is SCN1A, followed by MECP2 and CHD2. Studies employing exome sequencing and calling of both single nucleotide variants and copy number variants are associated with diagnostic yields of almost 50 %. Finally, we highlight three remarkable cases, each representing the oldest individual ever published with their genetic diagnosis, i. e., Angelman syndrome, Miller-Dieker syndrome, and CAMK2A-related disorder, and describe lessons learned from each of these adults.

Epigenetic genes and epilepsy - emerging mechanisms and clinical applications

An increasing number of epilepsies are being attributed to variants in genes with epigenetic functions. The products of these genes include factors that regulate the structure and function of chromatin and the placing, reading and removal of epigenetic marks, as well as other epigenetic processes. In this Review, we provide an overview of the various epigenetic processes, structuring our discussion around five function-based categories: DNA methylation, histone modifications, histone-DNA crosstalk, non-coding RNAs and chromatin remodelling. We provide background information on each category, describing the general mechanism by which each process leads to altered gene expression. We also highlight key clinical and mechanistic aspects, providing examples of genes that strongly associate with epilepsy within each class. We consider the practical applications of these findings, including tissue-based and biofluid-based diagnostics and precision medicine-based treatments. We conclude that variants in epigenetic genes are increasingly found to be causally involved in the epilepsies, with implications for disease mechanisms, treatments and diagnostics.

Impact of Genetic Testing on Therapeutic Decision-Making in Childhood-Onset Epilepsies-a Study in a Tertiary Epilepsy Center

We assessed the frequency of pediatric monogenic epilepsies and precision therapies at a tertiary epilepsy center. We analyzed medical records of children, born in 2006-2011 and followed at the Danish Epilepsy Center from January to December 2015; 357 patients were identified, of whom 27 without epilepsy and 35 with acquired brain damage were excluded. Of the remaining 295 children, 188 were consented for study inclusion and genetic testing. At inclusion, 86/188 had a preexisting genetic diagnosis and did not undergo further genetic testing. The 102 genetically unsolved patients underwent WES, which identified a (likely) pathogenic variant in eight patients and a highly relevant variant of unknown significance (VUS) in seven additional patients. Single nucleotide polymorphism array was performed in the remaining 87 patients and revealed no (likely) pathogenic copy number variants (CNVs). Patients with a genetic diagnosis had a significantly lower median age at seizure onset and more often had febrile seizures, status epilepticus, or neurodevelopmental impairment compared to those who remained genetically unsolved. Most common epilepsies were focal or multifocal epilepsies and developmental and epileptic encephalopathies (DDEs). Fifty-three patients, with a putative genetic diagnosis, were potentially eligible for precision therapy approaches. Indeed, genetic diagnosis enabled treatment adjustment in 32/53 (60%); 30/32 (93%) patients experienced at least a 50% reduction in seizure burden while only 4/32 (12.5%) became seizure-free. In summary, a genetic diagnosis was achieved in approximately 50% of patients with non-acquired epilepsy enabling precision therapy approaches in half of the patients, a strategy that results in > 50% reduction in seizure burden, in the majority of the treated patients.

Neurophysiological Findings in Neuronal Ceroid Lipofuscinoses

Neuronal ceroid lipofuscinoses (NCLs) are a heterogeneous group of neurodegenerative diseases, characterized by progressive cerebral atrophy due to lysosomal storage disorder. Common clinical features include epileptic seizures, progressive cognitive and motor decline, and visual failure, which occur over different time courses according to subtypes. During the latest years, many advances have been done in the field of targeted treatments, and in the next future, gene therapies and enzyme replacement treatments may be available for several NCL variants. Considering that there is rapid disease progression in NCLs, an early diagnosis is crucial, and neurophysiological features might have a key role for this purpose. Across the different subtypes of NCLs, electroencephalogram (EEG) is characterized by a progressive deterioration of cerebral activity with slowing of background activity and disappearance of spindles during sleep. Some types of heterogeneous abnormalities, diffuse or focal, prevalent over temporal and occipital regions, are described in many NCL variants. Photoparoxysmal response to low-frequency intermittent photic stimulation (IPS) is a typical EEG finding, mostly described in CLN2, CLN5, and CLN6 diseases. Visual evoked potentials (VEPs) allow to monitor the visual functions, and the lack of response at electroretinogram (ERG) reflects retinal neurodegeneration. Taken together, EEG, VEPs, and ERG may represent essential tools toward an early diagnosis of NCLs.

Treatment of Focal-Onset Seizures in Children: Should This Be More Etiology-Driven?

To accelerate the process of licensing antiseizure medication (ASM) in children, extrapolation of efficacy data for focal-onset seizures from adults to children ≥2 or ≥4 years of age is now accepted. We summarized the efficacy evidence from randomized, controlled trials that was used to grant approval for the pediatric indication of focal-onset seizures for the different ASMs available in Europe. Data from high-quality randomized, controlled trials in young children are limited, especially on the use of ASMs in monotherapy. Licensure trials are typically focused on seizure type irrespective of etiology or epilepsy syndrome. We elaborate on the importance of etiology- or syndrome-driven research and treatment, illustrating this with examples of childhood epilepsy syndromes characterized by predominantly focal-onset seizures. Some of these syndromes respond well to standard ASMs used for focal-onset seizures, but others would benefit from a more etiology- or syndrome-driven approach. Advances in molecular genetics and neuroimaging have made it possible to reveal the underlying cause of a child's epilepsy and tailor research and treatment. More high-quality randomized, controlled trials based on etiology or syndrome type are needed, including those assessing effects on cognition and behavior. In addition, study designs such as "N-of-1 trials" could elucidate possible new treatment options in rare epilepsies. Broadening incentives currently in place to stimulate the development and marketing of drugs for rare diseases (applicable to some epilepsy syndromes) to more common pediatric epilepsy types and syndromes might be a means to enable high-quality trials, and ultimately allow more evidence-based treatment in children.

Novel treatments in epilepsy guided by genetic diagnosis

In recent years, precision medicine has emerged as a new paradigm for improved and more individualized patient care. Its key objective is to provide the right treatment, to the right patient at the right time, by basing medical decisions on individual characteristics, including specific genetic biomarkers. In order to realize this objective researchers and physicians must first identify the underlying genetic cause; over the last 10 years, advances in genetics have made this possible for several monogenic epilepsies. Through next generation techniques, a precise genetic aetiology is attainable in 30-50% of genetic epilepsies beginning in the paediatric age. While committed in such search for novel genes carrying disease-causing variants, progress in the study of experimental models of epilepsy has also provided a better understanding of the mechanisms underlying the condition. Such advances are already being translated into improving care, management and treatment of some patients. Identification of a precise genetic aetiology can already direct physicians to prescribe treatments correcting specific metabolic defects, avoid antiseizure medicines that might aggravate functional consequences of the disease-causing variant or select the drugs that counteract the underlying, genetically determined, functional disturbance. Personalized, tailored treatments should not just focus on how to stop seizures but possibly prevent their onset and cure the disorder, often consisting of seizures and its comorbidities including cognitive, motor and behaviour deficiencies. This review discusses the therapeutic implications following a specific genetic diagnosis and the correlation between genetic findings, pathophysiological mechanisms and tailored seizure treatment, emphasizing the impact on current clinical practice.

Monogenic Epilepsies: Disease Mechanisms, Clinical Phenotypes, and Targeted Therapies

A monogenic etiology can be identified in up to 40% of people with severe epilepsy. To address earlier and more appropriate treatment strategies, clinicians are required to know the implications that specific genetic causes might have on pathophysiology, natural history, comorbidities, and treatment choices. In this narrative review, we summarize concepts on the genetic epilepsies based on the underlying pathophysiologic mechanisms and present the current knowledge on treatment options based on evidence provided by controlled trials or studies with lower classification of evidence. Overall, evidence robust enough to guide antiseizure medication (ASM) choices in genetic epilepsies remains limited to the more frequent conditions for which controlled trials and observational studies have been possible. Most monogenic disorders are very rare and ASM choices for them are still based on inferences drawn from observational studies and early, often anecdotal, experiences with precision therapies. Precision medicine remains applicable to only a narrow number of patients with monogenic epilepsies and may target only part of the actual functional defects. Phenotypic heterogeneity is remarkable, and some genetic mutations activate epileptogenesis through their developmental effects, which may not be reversed postnatally. Other genes seem to have pure functional consequences on excitability, acting through either loss- or gain-of-function effects, and these may have opposite treatment implications. In addition, the functional consequences of missense mutations may be difficult to predict, making precision treatment approaches considerably more complex than estimated by deterministic interpretations. Knowledge of genetic etiologies can influence the approach to surgical treatment of focal epilepsies. Identification of germline mutations in specific genes contraindicates surgery while mutations in other genes do not. Identification, quantification, and functional characterization of specific somatic mutations before surgery using CSF liquid biopsy or after surgery in brain specimens will likely be integrated in planning surgical strategies and reintervention after a first unsuccessful surgery as initial evidence suggests that mutational load may correlate with the epileptogenic zone. Promising future directions include gene manipulation by DNA or mRNA targeting; although most are still far from clinical use, some are in early phase clinical development.

Novel and emerging therapeutics for genetic epilepsies

INTRODUCTION

Disease-specific treatments are available only for a minority of patients with genetic epilepsies, while the rest are treated with anticonvulsants, which are ineffective in almost one-third of patients.

AREAS COVERED

Recently approved and the most effective emerging therapeutics under development for the treatment of genetic epilepsies are overviewed after systematic search and analysis of relevant literature.

EXPERT OPINION

New and emerging drugs for genetic epilepsies exploit one of the two approaches: inhibiting hyperactive brain foci through blocking excitatory or augmenting inhibitory neurotransmission, or correcting the underlying genetic defect. The first is limited by insufficient selectivity of available compounds, and the second by imperfection of currently used vectors of genetic material, unselective and transient transgene expression. Besides, the treatment may come too late, after structural abnormalities and epilepsy deterioration takes place. However, with recent improvements, we can expect to see soon gradual decline in the number of patients with therapy-resistant genetic epilepsies.

The pharmacological treatment of epilepsy: recent advances and future perspectives

The pharmacological armamentarium against epilepsy has expanded considerably over the last three decades, and currently includes over 30 different antiseizure medications. Despite this large armamentarium, about one third of people with epilepsy fail to achieve sustained seizure freedom with currently available medications. This sobering fact, however, is mitigated by evidence that clinical outcomes for many people with epilepsy have improved over the years. In particular, physicians now have unprecedented opportunities to tailor treatment choices to the characteristics of the individual, in order to maximize efficacy and tolerability. The present article discusses advances in the drug treatment of epilepsy in the last 5 years, focusing in particular on comparative effectiveness trials of second-generation drugs, the introduction of new pharmaceutical formulations for emergency use, and the results achieved with the newest medications. The article also includes a discussion of potential future developments, including those derived from advances in information technology, the development of novel precision treatments, the introduction of disease modifying agents, and the discovery of biomarkers to facilitate conduction of clinical trials as well as routine clinical management.

A Novel KCNA2 Variant in a Patient with Non-Progressive Congenital Ataxia and Epilepsy: Functional Characterization and Sensitivity to 4-Aminopyridine

Kv1.2 channels, encoded by the KCNA2 gene, are localized in the central and peripheral nervous system, where they regulate neuronal excitability. Recently, heterozygous mutations in KCNA2 have been associated with a spectrum of symptoms extending from epileptic encephalopathy, intellectual disability, and cerebellar ataxia. Patients are treated with a combination of antiepileptic drugs and 4-aminopyridine (4-AP) has been recently trialed in specific cases. We identified a novel variant in KCNA2, E236K, in a Serbian proband with non-progressive congenital ataxia and early onset epilepsy, treated with sodium valproate. To ascertain the pathogenicity of E236K mutation and to verify its sensitivity to 4-AP, we transfected HEK 293 cells with Kv1.2 WT or E236K cDNAs and recorded potassium currents through the whole-cell patch-clamp. In silico analysis supported the electrophysiological data. E236K channels showed voltage-dependent activation shifted towards negative potentials and slower kinetics of deactivation and activation compared with Kv1.2 WT. Heteromeric Kv1.2 WT+E236K channels, resembling the condition of the heterozygous patient, confirmed a mixed gain- and loss-of-function (GoF/LoF) biophysical phenotype. 4-AP inhibited both Kv1.2 and E236K channels with similar potency. Homology modeling studies of mutant channels suggested a reduced interaction between the residue K236 in the S2 segment and the gating charges at S4. Overall, the biophysical phenotype of E236K channels correlates with the mild end of the clinical spectrum reported in patients with GoF/LoF defects. The response to 4-AP corroborates existing evidence that KCNA2-disorders could benefit from variant-tailored therapeutic approaches, based on functional studies.