Mar 16, 2015 - new ones (VRK2 and FANCL). This serves to highlight the importance of large sample sizes in identifying new genes that may be involved in ...
Molecular genetics Recent advances in epilepsy Dr Vikas Dhiman of the National Institute of Mental Health and Neuro Sciences (Bangalore, India) explores advances in the molecular genetics of epilepsy
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n more than 50 per cent of people with epilepsy (PWE), the cause of the condition is not known (Pal, Pong and Chung, 2010). Previously, such epilepsies were diagnosed as ‘idiopathic’, leaving the patient with less scope for finding the reason behind his or her seizures and subsequently an appropriate treatment. The completion of the human genome project is one of several major advancements in gene sequencing technology over the last decade. Tremendous progress has been made in the field of the
When we think of genetic epilepsies, there is a spectrum of genotype-phenotype representation molecular genetics in epilepsy. There is now enough strong genetic evidence from multiple epidemiological and twin studies that that we can surmise that epilepsies previously categorised as ‘idiopathic’ actually have a genetic aetiology (Berg et al, 2010). In view of this, the International League Against Epilepsy (ILAE) has adopted the term ‘genetic generalised epilepsy (GGE)’ in Epilepsy Professional Spring 2015
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place of ‘idiopathic’ epilepsies. When we think of genetic epilepsies, there is a continuum spectrum of genotype-phenotype representation. On one end we see monogenic epilepsies with no (or minimal) environmental effect and, on the other end, complexly inherited, polygenic epilepsies with environmental interaction (Thomas and Berkovic, 2014). Of the genes known to play a role in the development of epilepsies, most were discovered as a result of studies of monogenic familial epilepsies. These follow more or less Mendelian forms of inheritance (on the former end of the spectrum). That said, in clinical practice, one tends to see more people presenting with sporadic epilepsies (the latter end of the spectrum). Over the last few years, understanding the molecular genetics of complex epilepsies remained the main focus of much research. Recent large international collaborations include the Epi4K consortium (Allen et al, 2013; International League Against Epilepsy Consortium on Complex Epilepsies, 2014). With these initiatives, researchers have made an exponential advancement in understanding the genetic aetiology of epilepsies. The main aim of this review
is to highlight the most recent and major advances in the field of molecular genetics in epilepsy, its
Researchers have made an exponential advancement in understanding the genetic aetiology of epilepsies impact in clinical practice and the future challenges in the field. I would like to summarise the most important discoveries made in the last five years in the field of epilepsy genetics.
Super eight – important discoveries
1. Paroxysmal kinesigenic dyskinesia (PKD) is the most common paroxysmal movement disorder and is often misdiagnosed as epilepsy. Three truncating mutations have been found in a newly discovered gene named PRRT2, which co-segregated exactly with the disease in eight Han Chinese families with a history of PKD. This gene codes for a proline-rich transmembrane protein 2 and is highly expressed in the developing brain, though the function of PRRT2 is not fully known (Chen et al, 2011).
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molecular genetics 2. For a long time, focal epilepsies were thought to arise from a localised structural lesion in the brain. It is now known that there are many focal epilepsy syndromes, which follow more or less Mendelian or complex forms of inheritance. The brain imaging is largely normal and underlying aetiology is unknown in these epilepsy syndromes. The seizures in these epilepsies arise from a focal area of the brain, such as: • The frontal lobe in autosomal dominant frontal lobe epilepsy (ADNFLE) • The temporal lobe in familial mesial temporal lobe epilepsy (FMTLE) and familial lateral temporal lobe epilepsy (FLTLE), collectively called familial temporal lobe epilepsy (FTLE) • The frontal, parietal or temporal lobe in familial focal epilepsy with variable foci (FFEVF) Recently, genetic mutations have been found in the DEPDC5 gene in multiple large and small families of ADNFLE, FFEVF and FMTLE (Ishida et al, 2013; Dibbens et al, 2013). More interestingly, a de novo mutation in the DEPDC5 gene has been found in a sporadic case of focal epilepsy, which implicates DEPDC5 in causing sporadic epilepsies (Dibbens et al, 2013). DEPDC5 encodes for a highly conserved protein presumably involved in the G protein-signalling pathway. Another important mutation in a family of ADNFLE with intellectual and psychiatric problems has been found in KCNT1, a sodium gated potassium channel gene (Heron et al, 2012). 3. Epileptic encephalopathies (EEs) are a heterogeneous group of severe epilepsies characterised by an early onset of seizures with cognitive and behavioural manifestations. The aetiology of most EEs is largely
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unknown. A large multinational consortium – namely Epi4K – studied 264 probands of infantile spasms and Lennox-Gastaut syndrome and their parents. Findings identified de novo mutations in GABRB3 and ALG13 genes with high statistical significance (Allen et al, 2013). Similarly, targeted sequencing analysis of 65 genes was used to assess about 500 patients in a mixed
Mutations in EEs make de novo mutagenesis an important mechanism in causing epilepsy group of EE cases. The analysis showed de novo mutations in CHD2 and SYNGAP1 genes in six and five individuals respectively (Carvill et al, 2013a). CHD2 encodes for a chromo domain DNA helicase binding protein, which has a role in modulating the chromatin structure. SYNGAP1 encodes synaptic Ras GTPaseactivating protein 1, which is involved in synaptic functioning and has been implicated in children with intellectual disability. Malignant migrating partial seizures of infancy (MMPSI) is a rare epileptic encephalopathy associated with poor outcomes. A de novo gain-of-function mutation in the KCNT1 gene has been reported in six unrelated cases of MMPSI (Barcia et al, 2012). KCNT1 has a non-conducting function; it interacts with cytoplasmic proteins, which are involved in developmental pathways. The increasing discovery of mutations in EEs make de novo mutagenesis an important mechanism in causing epilepsy. This warrants further research into this mechanism in other forms of epilepsy.
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4. Multiple large collaborative studies published in a single year (2013) in Nature Genetics have shown the role of pathogenic variants in the GRIN2A gene. This gene encodes for N-methyl-D-aspartate (NMDA) glutamate receptor α2 subunit in epilepsy-aphasia spectrum disorders (Carvill et al, 2013b; Lemke et al, 2013; Lesca et al, 2013). This heterogeneous group of childhood epilepsies range from relatively benign childhood epilepsy with centrotemporal spikes (BECTS) to atypical rolandic epilepsy, LandauKleffner syndrome (LKS) and EE with continuous spike and wave during slow wave sleep (CSWS). Such strong evidence provides crucial insights into the underlying pathomechanisms of these syndromes. These insights may lead to the development of novel pharmacological treatments. 5. As stated previously, the genetic determinants in more common yet more complex generalised epilepsies are largely unknown. In view of this, the International League Against Epilepsy Consortium on Complex Epilepsies published one of the largest genome-wide association metaanalyses done in epilepsy. The initiative
The genetic determinants in more common yet more complex generalised epilepsies are largely unknown included 8,696 people with complex epilepsies and 26,157 control individuals. The study highlighted the potential roles played by some already known genes (SCN1A, PCDH7) and some new ones (VRK2 and FANCL). This serves to highlight the importance of Epilepsy Professional Spring 2015
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molecular genetics large sample sizes in identifying new genes that may be involved in complex disorders like epilepsy (International League Against Epilepsy Consortium on Complex Epilepsies, 2014). 6. Progressive myoclonic epilepsies (PME) are a rare and debilitating group of disorders characterised by action myoclonus, tonic-clonic seizures and ataxia. Patients with PME have a very poor prognosis and death usually occurs young (Muona et al, 2015). Currently, the only treatment options available for such patients represent symptomatic care, such as antiepileptic drugs (AEDs). Recently, de novo mutations in KCNC1 gene – which codes for Kv3.1 subunit of voltage gated potassium channel – have been found in a large cohort of PME patients. This is probably the largest genetic study involving PME patients across the globe. Possibly, in the near future, more understanding of the aetiology of PMEs would enable us to develop new treatment strategies for this devastating condition. 7. The genetic causes of febrile seizures are fairly well established. SCN1A testing is now widely available, especially in the diagnosis of Dravet syndrome (Ottman et al, 2010). More recently, a new gene – STX1B, which encodes for a presynaptic protein – has been strongly implicated in febrile seizures and fever-associated epilepsy syndromes (Schubert et al, 2014). This gene has a distinct function; it is involved in the presynaptic release machinery of the neurotransmitters. This novel finding links febrile seizures and fever-related epilepsy syndromes to a new class of epilepsies called ‘synaptopathies’ (alongside historically known channelopathies). Interestingly, genetic variants associated with febrile seizures following administration of the MMR (measles, mumps, rubella) vaccine have
been identified. Genome-wide association scans done in over 4,000 subjects demonstrated a significant association of two loci harbouring two novel genes. Namely, these were interferon stimulated IFI44L gene and measles virus receptor CD46 gene (Feenstra et al, 2014). 8. We have seen a rapid increase in our understanding of the importance
We have seen a rapid increase in our understanding of epigenetic mechanisms in health and disease of epigenetic mechanisms in health and disease. Investigators are starting to understand the role of epigenetic mechanisms – such as DNA methylation, non-coding RNA, microRNA – in causing epilepsies. A recent study (Miller-Delaney et al, 2014) analysed patients of drugresistant temporal lobe epilepsy having mild or severe forms of hippocampal sclerosis. Study findings highlighted the whole genome pattern of DNA methylation and microRNA (miRNA) in these cases.
Benchside manner
There has been a flood of genetic information in the medical literature over the last decade and this will only continue in the near future. It is important to take these advancements from the bench to the bedside. There are several genetic tests available in clinical practice to diagnose specific types of epilepsies. Genetic testing is acquiring an important place in the armamentarium of diagnostic tests used in treating epilepsy patients. These tests may be done to make a diagnosis of genetic epilepsy in a person already known or suspected to
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molecular genetics have epilepsy. They may also be done to predict the occurrence of epilepsy in a person with a family history of epilepsy (Ottman et al, 2010). Clinical genetic testings are usually done in a certified clinical laboratory equipped with quality-control standards, accurate methods to interpret results and the facility to offer genetic counselling to the
Sometimes genetic test results have important implications for marriage and reproductive decisions patients. A positive test often makes patients and family members feel relieved. They know the genetic cause of their epilepsy and can avoid unnecessary, expensive and often invasive investigations. In less developed countries, healthcare costs are largely met by the patient and not by insurance companies or the governmental agencies. This can lead to financial burden on the patient and the family. The situation becomes more critical if the patient requires more costly investigations such as 3T MRI, positron emission tomography (PET) scan, magnetoencephalography (MEG) or intracranial EEG recordings. Positive genetic tests results can avoid such situations, especially in economically less stable families. Sometimes genetic test results have important implications for marriage and reproductive decisions. Marriage between two individuals having a carrier mutation for a disorder can pose a 25 per cent risk in every pregnancy that the offspring might receive both recessive genes and exhibit the disease. This situation is more important in marriages where
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both partners share a common ancestor. In these cases, the chances of developing autosomal recessive disorders are much higher due to sharing of the common genetic pool. Therefore, genetic testing should be advocated before marriage and conception in every couple where there is a history of multiple family members affected by epilepsy. A positive test result can also lead to psychological stress and sometimes discrimination in cases of a person’s health insurance, job and social life. It can also lead to guilt in parents, who often feel responsible for the disease in their child (Pal, Pong and Chung, 2010). A special report from the ILAE genetics commission provides a list of the genes implicated in epilepsy. Listed are the genes with high clinical validity and clinical utility for diagnostic and predictive testing in an individual with epilepsy or suspected to develop epilepsy (Ottman et al, 2010). Some of the most useful genes in the clinical testing are: • SCN1A for severe myoclonic epilepsy of infancy or Dravet syndrome • PCDH19 for epilepsy and learning disabilities (limited to females) • CHRNA4 and CHRNB2 for autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE) and • SLC2A1 in epilepsy with paroxysmal exercise induced dyskinesia In view of the rapid rate of development in epilepsy genetics research, many more genes are going to add to this list. The aim of the treating epileptologist and the clinical geneticist should be to ensure maximum benefit of any genetic testing to the patient and their family members (Helbig et al, 2008). This can epilepsy.org.uk issue thirty-six
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be achieved by carefully selecting patients for genetic testing and the type of test, correctly interpreting the results and offering effective pre- and post-test genetic counselling.
Future challenges
Most of the common epilepsies follow a complex form of inheritance, which is determined by complex interactions of gene/genes and environmental factors. In such scenarios, the genotype-phenotype correlation poses a major challenge for both epileptologists and scientists in understanding the molecular basis of epilepsies. There has been new and exciting information emerging from different forms of epilepsy. Understanding the molecular mechanisms of more common epilepsy syndromes – such as juvenile myoclonic epilepsy (JME) and childhood absence epilepsy (CAE) – continues to pose a major challenge to the epilepsy researchers. The role of epigenetic mechanisms should be studied in understanding these syndromes. Another important challenge – which is more relevant in the context of developing countries – is the high cost of genetic testing. This cost has been decreasing quite rapidly
Another important challenge in the context of developing countries is the high cost of genetic testing – but genetic testing has to go a long way before becoming a regular laboratory test for epilepsy patients. Another important concern is the importance of taking a detailed family history, which has been underestimated in many clinical Epilepsy Professional Spring 2015
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settings leading to inappropriate diagnosis and management of the
The advancement of molecular genetic techniques has propelled epilepsy genetics research to an all-time high patients.Young clinicians should be trained and sensitised to take a detailed family history of every person with seizures who comes to the clinic.
Conclusion
Understanding the molecular basis of epilepsies can provide crucial information in understanding the pathophysiology of epilepsies. This can have direct and indirect implications in
Further reading Allen AS et al (2013). ‘De novo mutations in epileptic encephalopathies’. Nature (501) pp. 217–21 Barcia G et al (2012). ‘De novo gain-of-function KCNT1 channel mutations cause malignant migrating partial seizures of infancy’. Nature genetics (44) pp. 1,255–9 Berg AT et al (2010). ‘Revised terminology and concepts for organization of seizures and epilepsies: report of the ILAE Commission on Classification and Terminology, 2005-2009’. Epilepsia (Vol 51, Issue 4) pp. 676–85 Carvill GL et al (2013a). ‘Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1’. Nature genetics (45) pp. 825–30 Carvill GL et al (2013b). ‘GRIN2A mutations cause epilepsy-aphasia spectrum disorders’. Nature genetics (45) pp. 1,073–6 Chen WJ et al (2011). ‘Exome sequencing identifies truncating mutations in PRRT2 that cause paroxysmal kinesigenic dyskinesia’. Nature genetics (43) 1,252–1,255 Dibbens LM et al (2013). ‘Mutations in DEPDC5 cause familial focal epilepsy with variable foci’. Nature genetics (45) pp. 546–51 Feenstra B et al (2014). ‘Common variants associated with general and MMR vaccine-related febrile seizures’. Nature genetics (46) 1,274–82 Helbig I et al (2008). ‘Navigating the channels and beyond: unravelling the genetics of the epilepsies’. The Lancet Neurology (Vol 7, Issue 3) pp. 231–45 Heron SE et al (2012). ‘Missense mutations in the sodium-gated potassium channel gene KCNT1 cause severe autosomal dominant nocturnal frontal lobe epilepsy’. Nature genetics (44) pp. 1,188–90
terms of genetic testing, new drug development and treatment personalisation (Thomas and Berkovic, 2014). Although much remains to be done, the rapid advancement of molecular genetic techniques has propelled epilepsy genetics research to an all-time high. The goal of epilepsy clinicians and researchers remains to understand the mechanisms of epilepsies more and more clearly. Only then can it be meaningfully applied for the betterment of people with epilepsy (Thomas and Berkovic, 2014).
Dr Vikas Dhiman National Institute of Mental Health and Neuro Sciences (NIMHANS) Bangalore India International League Against Epilepsy Consortium on Complex Epilepsies (2014). ‘Genetic determinants of common epilepsies: a meta-analysis of genome-wide association studies’. The Lancet Neurology (vol 13, Issue 9) pp. 893–903 Ishida S et al (2013). ‘Mutations of DEPDC5 cause autosomal dominant focal epilepsies’. Nature genetics (45) pp. 552–5 Lemke JR et al (2013). ‘Mutations in GRIN2A cause idiopathic focal epilepsy with rolandic spikes’. Nature genetics (45) pp. 1,067–72 Lesca G et al (2013). ‘GRIN2A mutations in acquired epileptic aphasia and related childhood focal epilepsies and encephalopathies with speech and language dysfunction’. Nature genetics (45) pp. 1,061–6 Miller-Delaney SF et al (2014). ‘Differential DNA methylation profiles of coding and non-coding genes define hippocampal sclerosis in human temporal lobe epilepsy’. Brain: a journal of neurology (Vol 138, Issue 3) pp. 616–31 Muona M et al (2015). A recurrent de novo mutation in KCNC1 causes progressive myoclonus epilepsy. Nature genetics (47) pp. 39–46 Ottman R et al (2010). ‘Genetic testing in the epilepsies--report of the ILAE Genetics Commission’. Epilepsia (Vol 51, Issue 4) pp. 655–70 Pal DK, Pong AW and Chung WK (2010). ‘Genetic evaluation and counseling for epilepsy’. Nature reviews Neurology (6) pp. 445–53 Schubert, J. et al. Mutations in STX1B, encoding a presynaptic protein, cause fever-associated epilepsy syndromes. Nature genetics (46) pp. 1,327–32 Thomas R H and Berkovic SF (2014). ‘The hidden genetics of epilepsy-a clinically important new paradigm’. Nature reviews Neurology (10) 283–92
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