A new molecular mechanism for severe myoclonic epilepsy of infancy: Exonic deletions in SCN1A

Analysis of SCN1A mutation and parental origin in patients with Dravet syndrome

Dravet syndrome (DS) or severe myoclonic epilepsy of infancy is an intractable epileptic syndrome that is caused by mutations in the neuronal voltage-gated sodium channel alpha1 subunit gene SCN1A. We investigated SCN1A mutations in 63 Chinese patients with DS and analyzed its inheritance. Genomic DNA was extracted from peripheral blood lymphocytes of DS patients and their available parents. The SCN1A open reading frame sequence was analyzed by PCR-DNA sequencing and multiple ligation-dependent probe amplication (MLPA). If the mutation was de novo, we used allele-specific PCR (AS-PCR) to determine the parental origin. Of the 63 patients examined, 49 unrelated patients had SCN1A mutations. The mutation rate was 77.8% (49 of 63), in which 61.2% (30 of 49) were truncation mutations. The mutations included 19 missense mutations, 14 frame-shift mutations, 6 nonsense mutations, 8 splice-site mutations. Through MLPA analysis, deletions or duplications of large fragments accounted for 12.5% (2 of 16) in PCR-sequencing-negative patients. By testing parents for the mutation, 40 mutations were found to be de novo and one mutation was inherited from a mother who was mosaic for a mutation. By AS-PCR analysis in 12 patients with de novo mutations, 10 were confirmed paternal in origin and 2 were maternal in origin. Thirty of the SCN1A mutations reported here have not been previously reported. Approximately 80% of Chinese DS patients have SCN1A mutations. MLPA analysis was essential for PCR-sequencing-negative patients. The majority of SCN1A mutations were de novo, most of which were paternal origin.

Genetic testing in the epilepsies--report of the ILAE Genetics Commission

In this report, the International League Against Epilepsy (ILAE) Genetics Commission discusses essential issues to be considered with regard to clinical genetic testing in the epilepsies. Genetic research on the epilepsies has led to the identification of more than 20 genes with a major effect on susceptibility to idiopathic epilepsies. The most important potential clinical application of these discoveries is genetic testing: the use of genetic information, either to clarify the diagnosis in people already known or suspected to have epilepsy (diagnostic testing), or to predict onset of epilepsy in people at risk because of a family history (predictive testing). Although genetic testing has many potential benefits, it also has potential harms, and assessment of these potential benefits and harms in particular situations is complex. Moreover, many treating clinicians are unfamiliar with the types of tests available, how to access them, how to decide whether they should be offered, and what measures should be used to maximize benefit and minimize harm to their patients. Because the field is moving rapidly, with new information emerging practically every day, we present a framework for considering the clinical utility of genetic testing that can be applied to many different syndromes and clinical contexts. Given the current state of knowledge, genetic testing has high clinical utility in few clinical contexts, but in some of these it carries implications for daily clinical practice.

Severe epilepsy syndromes of early childhood: the link between genetics and pathophysiology with a focus on SCN1A mutations

Advances in genetics have increased our understanding of the underlying pathophysiologic mechanisms that cause severe epilepsy syndromes of early childhood. Many of the mutations associated with these syndromes are located in genes coding for ion channels or their accessory subunits, giving rise to the concept of epilepsy ;;channelopathies.'' In particular, the SCN1A gene coding for the pore-forming a-subunit of the voltage-gated sodium channel Na(V)1.1 appears to be a common target for epilepsy syndrome-specific mutations. An SCN1A mutation can potentially result in either a gain or loss of sodium channel function. Epilepsies linked to SCN1A mutations range from a relatively benign syndrome called generalized epilepsy with febrile seizures plus to severe childhood epilepsies such as severe myoclonic epilepsy of infancy (Dravet syndrome). The availability of genetic tests for SCN1A mutations is expanding awareness of the spectrum of diseases mediated by this gene and is beginning to permit genotype- phenotype correlations. Eventually, such information might enable clinicians to select an appropriate therapeutic regimen for patients with specific epilepsy gene mutations.

Genetic basis in epilepsies caused by malformations of cortical development and in those with structurally normal brain

Epilepsy is the most common neurological disorder affecting young people. The etiologies are multiple and most cases are sporadic. However, some rare families with Mendelian inheritance have provided evidence of genes' important role in epilepsy. Two important but apparently different groups of disorders have been extensively studied: epilepsies associated with malformations of cortical development (MCDs) and epilepsies associated with a structurally normal brain (or with minimal abnormalities only). This review is focused on clinical and molecular aspects of focal cortical dysplasia, polymicrogyria, periventricular nodular heterotopia, subcortical band heterotopia, lissencephaly and schizencephaly as examples of MCDs. Juvenile myoclonic epilepsy, childhood absence epilepsy, some familial forms of focal epilepsy and epilepsies associated with febrile seizures are discussed as examples of epileptic conditions in (apparently) structurally normal brains.

Dravet syndrome or genetic (generalized) epilepsy with febrile seizures plus?

Dravet syndrome and genetic epilepsy with febrile seizures plus (GEFS+) can both arise due to mutations of SCN1A, the gene encoding the alpha 1 pore-forming subunit of the sodium channel. GEFS+ refers to a familial epilepsy syndrome where at least two family members have phenotypes that fit within the GEFS+ spectrum. The GEFS+ spectrum comprises a range of mild to severe phenotypes varying from classical febrile seizures to Dravet syndrome. Dravet syndrome is a severe infantile onset epilepsy syndrome with multiple seizure types, developmental slowing and poor outcome. More than 70% of patients with Dravet syndrome have mutations of SCN1A; these include both truncation and missense mutations. In contrast, only 10% of GEFS+ families have SCN1A mutations and these comprise missense mutations. GEFS+ has also been associated with mutations of genes encoding the sodium channel beta 1 subunit, SCN1B, and the GABA(A) receptor gamma 2 subunit, GABRG2. The phenotypic heterogeneity that is characteristic of GEFS+ families is likely to be due to modifier genes. Interpretation of the significance of a SCN1A missense mutation requires a thorough understanding of the phenotypes in the GEFS+ spectrum whereas a de novo truncation mutation is likely to be associated with a severe phenotype. Early recognition of Dravet syndrome is important as aggressive control of seizures may improve developmental outcome.

SCN1A duplications and deletions detected in Dravet syndrome: implications for molecular diagnosis

OBJECTIVE

We aimed to determine the type, frequency, and size of microchromosomal copy number variations (CNVs) affecting the neuronal sodium channel α 1 subunit gene (SCN1A) in Dravet syndrome (DS), other epileptic encephalopathies, and generalized epilepsy with febrile seizures plus (GEFS+).

METHODS

Multiplex ligation-dependent probe amplification (MLPA) was applied to detect SCN1A CNVs among 289 cases (126 DS, 97 GEFS+, and 66 with other phenotypes). CNVs extending beyond SCN1A were further characterized by comparative genome hybridization (array CGH).

RESULTS

Novel SCN1A CNVs were found in 12.5% of DS patients where sequence-based mutations had been excluded. We identified the first partial SCN1A duplications in two siblings with typical DS and in a patient with early-onset symptomatic generalized epilepsy. In addition, a patient with DS had a partial SCN1A amplification of 5-6 copies. The remaining CNVs abnormalities were four partial and nine whole SCN1A deletions involving contiguous genes. Two CNVs (a partial SCN1A deletion and a duplication) were inherited from a parent, in whom there was mosaicism. Array CGH showed intragenic deletions of 90 kb and larger, with the largest of 9.3 Mb deleting 49 contiguous genes and extending beyond SCN1A.

DISCUSSION

Duplication and amplification involving SCN1A are now added to molecular mechanisms of DS patients. Our findings showed that 12.5% of DS patients who are mutation negative have MLPA-detected SCN1A CNVs with an overall frequency of about 2-3%. MLPA is the established second-line testing strategy to reliably detect all CNVs of SCN1A from the megabase range down to one exon. Large CNVs extending outside SCN1A and involving contiguous genes can be precisely characterized by array CGH.

Sporadic infantile epileptic encephalopathy caused by mutations in PCDH19 resembles Dravet syndrome but mainly affects females

Dravet syndrome (DS) is a genetically determined epileptic encephalopathy mainly caused by de novo mutations in the SCN1A gene. Since 2003, we have performed molecular analyses in a large series of patients with DS, 27% of whom were negative for mutations or rearrangements in SCN1A. In order to identify new genes responsible for the disorder in the SCN1A-negative patients, 41 probands were screened for micro-rearrangements with Illumina high-density SNP microarrays. A hemizygous deletion on chromosome Xq22.1, encompassing the PCDH19 gene, was found in one male patient. To confirm that PCDH19 is responsible for a Dravet-like syndrome, we sequenced its coding region in 73 additional SCN1A-negative patients. Nine different point mutations (four missense and five truncating mutations) were identified in 11 unrelated female patients. In addition, we demonstrated that the fibroblasts of our male patient were mosaic for the PCDH19 deletion. Patients with PCDH19 and SCN1A mutations had very similar clinical features including the association of early febrile and afebrile seizures, seizures occurring in clusters, developmental and language delays, behavioural disturbances, and cognitive regression. There were, however, slight but constant differences in the evolution of the patients, including fewer polymorphic seizures (in particular rare myoclonic jerks and atypical absences) in those with PCDH19 mutations. These results suggest that PCDH19 plays a major role in epileptic encephalopathies, with a clinical spectrum overlapping that of DS. This disorder mainly affects females. The identification of an affected mosaic male strongly supports the hypothesis that cellular interference is the pathogenic mechanism.

A catalog of SCN1A variants

Over the past 10 years mutations in voltage-gated sodium channels (Na(v)s) have become closely associated with inheritable forms of epilepsy. One isoform in particular, Na(v)1.1 (gene symbol SCN1A), appears to be a superculprit, registering with more than 330 mutations to date. The associated phenotypes range from benign febrile seizures to extremely serious conditions, such as Dravet's syndrome (SMEI). Despite the wealth of information, mutational analyses are cumbersome, owing to inconsistencies among the Na(v)1.1 sequences to which different research groups refer. Splicing variability is the core problem: Na(v)1.1 co-exists in three isoforms, two of them lack 11 or 28 amino acids compared to full-length Na(v).1.1. This review establishes a standardized nomenclature for Na(v)1.1 variants so as to provide a platform from which future mutation analyses can be started without need for up-front data normalization. An online resource--SCN1A infobase--is introduced.

Forty Years From Markers to Genes

There have been incredible advances made in human genetics over the past 40 years. I have set out in the next few pages to describe just some of these changes and to illustrate how they unfolded through my own experiences.

SCN1A, SCN1B, and GABRG2 gene mutation analysis in Chinese families with generalized epilepsy with febrile seizures plus

Generalized epilepsy with febrile seizures plus (GEFS+; MIM#604233) is a familial epilepsy syndrome characterized by phenotypic and genetic heterogeneity. It was associated with mutations in the neuronal voltage-gated sodium channel subunit gene (SCN1A, SCN2A, SCN1B) and ligand-gated gamma aminobutyric acid receptors genes (GABRG2, GABRD). We investigated the roles of SCN1A, SCN1B, and GABRG2 mutations in the etiology of Chinese GEFS+ families. Genomic deoxyribonucleic acid (DNA) was extracted from peripheral blood lymphocytes of 23 probands and their family members. The sequences of SCN1A, SCN1B, and GABRG2 genes were analyzed by polymerase chain reaction (PCR) and direct sequencing. The major phenotypes of affected members in the 23 GEFS+ families exhibited FS and FS+, whereas rare phenotypes afebrile generalized tonic-clonic seizures (AGTCS), myoclonic-astatic epilepsy (MAE), and partial seizures were also observed. A novel SCN1A mutation, p.N935H, was identified in one family and another novel mutation in GABRG2, p.W390X, in another family. However, no SCN1B mutation was identified. The combined frequency of SCN1A, SCN1B, and GABRG2 mutations was 8.7% (2/23), extending the distribution of SCN1A and GABRG2 mutations to Chinese GEFS+ families. There were still unidentified genes contributing to the pathogenesis of GEFS+.

Epileptic syndromes in infancy and childhood

PURPOSE OF REVIEW

The aim of this article is to review new epilepsy syndromes, acquire a new understanding of older ones and emphasize the impact of this concept on basic research regarding aetiology and treatment.

RECENT FINDINGS

In addition to those included in the classification of the International League Against Epilepsy, new epilepsy syndromes comprise febrile seizures plus, benign familial neonatal-infantile seizures (BFNIS), benign infantile focal epilepsy with midline spikes and waves during sleep (BFIS), malignant migrating partial seizures in infancy, devastating epilepsy in school age children and late onset cryptogenic spasms. Genetics played a central role in identifying some new entities (BFNIS, BFIS with choreoathetosis), to delineate older syndromes (Dravet syndrome and myoclonic astatic epilepsy) and determine their mechanisms (infantile spasms, pyridoxine dependent seizures, neonatal encephalopathy with suppression bursts).

SUMMARY

A significant number of children, mainly infants, do not fit in any of the described epilepsy syndromes. Still many patients with infantile epilepsy require the identification of cause or recognition of an epilepsy syndrome.

How do mutant Nav1.1 sodium channels cause epilepsy?

Voltage-gated sodium channels comprise pore-forming alpha subunits and auxiliary beta subunits. Nine different alpha subtypes, designated Nav1.1-Nav1.9 have been identified in excitable cells. Nav1.1, 1.2 and 1.6 are major subtypes in the adult mammalian brain. More than 200 mutations in the Nav1.1 alpha subtype have been linked to inherited epilepsy syndromes, ranging in severity from the comparatively mild disorder Generalized Epilepsy with Febrile Seizures Plus to the epileptic encephalopathy Severe Myoclonic Epilepsy of Infancy. Studies using heterologous expression and functional analysis of recombinant Nav1.1 channels suggest that epilepsy mutations in Nav1.1 may cause either gain-of-function or loss-of-function effects that are consistent with either increased or decreased neuronal excitability. How these diverse effects lead to epilepsy is poorly understood. This review summarizes the data on sodium channel mutations and epilepsy and builds a case for the hypothesis that most Nav1.1 mutations have their ultimate epileptogenic effects by reducing Nav1.1-mediated whole cell sodium currents in GABAergic neurons, resulting in widespread loss of brain inhibition, an ideal background for the genesis of epileptic seizures.

Deletions or duplications in KCNQ2 can cause benign familial neonatal seizures

BACKGROUND

Benign familial neonatal seizures are most often caused by mutations in the voltage-gated potassium channel subunit gene KCNQ2. More than 60 mutations have been described in BFNS families, approximately half of which lead to protein truncation. The hypothesis of this study was that deletion or duplication of >or=1 exons of KCNQ2 could cause BFNS in cases without coding or splicing mutations.

METHODS

Multiplex ligation-dependent probe amplification (MLPA) was used to test a group of 21 unrelated patients with clinical features consistent with either BFNS, benign familial neonatal-infantile seizures or sporadic neonatal seizures, for exonic deletions and duplications.

RESULTS

Three deletions and one duplication mutation were identified in four familial cases and cascade testing of their available family members showed that the mutations segregated with the phenotype in each family. The junction fragment for one of the deletions was amplified by PCR and sequenced to characterise the breakpoint and verify that a deletion had occurred.

CONCLUSIONS

Submicroscopic deletions or duplications of KCNQ2 are seen in a significant proportion of BFNS families: four of nine (44%) cases previously testing negative for coding or splice site mutation by sequencing KCNQ2 and KCNQ3. MLPA is an efficient second-tier testing strategy for KCNQ2 to identify pathogenic intragenic mutations not detectable by conventional DNA sequencing methods.

Idiopathic epilepsies with seizures precipitated by fever and SCN1A abnormalities

PURPOSE

SCN1A is the most clinically relevant epilepsy gene, most mutations lead to severe myoclonic epilepsy of infancy (SMEI) and generalized epilepsy with febrile seizures plus (GEFS+). We studied 132 patients with epilepsy syndromes with seizures precipitated by fever, and performed phenotype-genotype correlations with SCN1A alterations.

METHODS

We included patients with SMEI including borderline SMEI (SMEB), GEFS+, febrile seizures (FS), or other seizure types precipitated by fever. We performed a clinical and genetic study focusing on SCN1A, using dHPLC, gene sequencing, and MLPA to detect genomic deletions/duplications on SMEI/SMEB patients.

RESULTS

We classified patients as: SMEI/SMEB = 55; GEFS+= 26; and other phenotypes = 51. SCN1A analysis by dHPLC/sequencing revealed 40 mutations in 37 SMEI/SMEB (67%) and 3 GEFS+ (11.5%) probands. MLPA showed genomic deletions in 2 of 18 SMEI/SMEB. Most mutations were de novo (82%). SMEB patients carrying mutations (8) were more likely to have missense mutations (62.5%), conversely SMEI patients (31) had more truncating, splice site or genomic alterations (64.5%). SMEI/SMEB with truncating, splice site or genomic alterations had a significantly earlier age of onset of FS compared to those with missense mutations and without mutations (p = 0.00007, ANOVA test). None of the remaining patients with seizures precipitated by fever carried SCN1A mutations.

CONCLUSION

We obtained a frequency of 71%SCN1A abnormalities in SMEI/SMEB and of 11.5% in GEFS+ probands. MLPA complements DNA sequencing of SCN1A increasing the mutation detection rate. SMEI/SMEB with truncating, splice site or genomic alterations had a significantly earlier age of onset of FS. This study confirms the high sensitivity of SCN1A for SMEI/SMEB phenotypes.

Channelopathies in idiopathic epilepsy

Approximately 70% of all patients with epilepsy lack an obvious extraneous cause and are presumed to have a predominantly genetic basis. Both familial and de novo mutations in neuronal voltage-gated and ligand-gated ion channel subunit genes have been identified in autosomal dominant epilepsies. However, patients with dominant familial mutations are rare and the majority of idiopathic epilepsy is likely to be the result of polygenic susceptibility alleles (complex epilepsy). Data on the identity of the genes involved in complex epilepsy is currently sparse but again points to neuronal ion channels. The number of genes and gene families associated with epilepsy is rapidly increasing and this increase is likely to escalate over the coming years with advances in mutation detection technologies. The genetic heterogeneity underlying idiopathic epilepsy presents challenges for the rational selection of therapies targeting particular ion channels. Too little is currently known about the genetic architecture of the epilepsies, and genetic testing for the known epilepsy genes remains costly. Pharmacogenetic studies have yet to explain why 30% of patients do not respond to the usual antiepileptic drugs. Despite this, the recognition that the idiopathic epilepsies are a group of channelopathies has, to a limited extent, explained the therapeutic action of the common antiepileptic drugs and has assisted clinical diagnosis of some epilepsy syndromes.

The spectrum of SCN1A-related infantile epileptic encephalopathies

The relationship between severe myoclonic epilepsy of infancy (SMEI or Dravet syndrome) and the related syndrome SMEI-borderland (SMEB) with mutations in the sodium channel alpha 1 subunit gene SCN1A is well established. To explore the phenotypic variability associated with SCN1A mutations, 188 patients with a range of epileptic encephalopathies were examined for SCN1A sequence variations by denaturing high performance liquid chromatography and sequencing. All patients had seizure onset within the first 2 years of life. A higher proportion of mutations were identified in patients with SMEI (52/66; 79%) compared to patients with SMEB (25/36; 69%). By studying a broader spectrum of infantile epileptic encephalopathies, we identified mutations in other syndromes including cryptogenic generalized epilepsy (24%) and cryptogenic focal epilepsy (22%). Within the latter group, a distinctive subgroup designated as severe infantile multifocal epilepsy had SCN1A mutations in three of five cases. This phenotype is characterized by early onset multifocal seizures and later cognitive decline. Knowledge of an expanded spectrum of epileptic encephalopathies associated with SCN1A mutations allows earlier diagnostic confirmation for children with these devastating disorders.

Channel, neuronal and clinical function in sodium channelopathies: from genotype to phenotype

What is the relationship between sodium channel function, neuronal function and clinical status in channelopathies of the nervous system? Given the central role of sodium channels in the generation of neuronal activity, channelopathies involving sodium channels might be expected to cause either enhanced sodium channel function and neuronal hyperexcitability associated with positive clinical manifestations such as seizures, or attenuated channel function and neuronal hypoexcitability associated with negative clinical manifestations such as paralysis. In this article, I review observations showing that changes in neuronal function and clinical status associated with channelopathies are not necessarily predictable solely from the altered physiological properties of the mutated channel itself. I discuss evidence showing that cell background acts as a filter that can strongly influence the effects of ion channel mutations.