Practical overview of genetics in childhood epilepsies...Genes involves in both mild and severe epilepsy phenotypes Gene Mild phenotype Severe phenotype SCN1A GEFS+ Dravet SCN1B GEFS+

Practical overview of genetics in childhood epilepsies

Dr Gaëtan LescaDepartment of Medical Genetics, Lyon

University Hospital, France

Gene discovery in Mendelian epilepsies (Helbig et al., 2016)

AchR genes and Autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE)

(Scheffer et al., 1994)

• Mutation in 3 genes :– CHRNA4 (Scheffer et al., 1995, Philipps et al.,

1995, Steinlein et al., 1995)

– CHRNB2 (Rempel et al., 1998)

– CHRNA2 (Aridon et al., 2006).

AchR genes and Autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE)

(Scheffer et al., 1994)

• Mutation in 3 genes :– CHRNA4 (Scheffer et al., 1995, Philipps et al.,

1995, Steinlein et al., 1995)

– CHRNB2 (Rempel et al., 1998)

– CHRNA2 (Aridon et al., 2006).

Conti et al., 2015

➢ Increased sensitivity to Acetylcholine

Self-limiting epilepsies in infancy(Benign familial epilepsies)

Lauxmann et al., 2013


Benign Familial Neonatal Epilepsy

1 day

3 months

1 year

KCNQ2> KCNQ3

SCN2A

1998



Benign Familial Neonatal Infantile Epilepsy

1 day

3 months

1 year

KCNQ2> KCNQ3

SCN2A

SCN2A

2004




Benign Familial Infantile Epilepsy

1 day

3 months

1 year

KCNQ2> KCNQ3

SCN2A

PRRT2

SCN2A

2011




Benign Familial Infantile Epilepsy

1 day

3 months

1 year

KCNQ2> KCNQ3

SCN2A

PRRT2

Cognitive impairment

No(only if homozygous)

No

Rare (5%), usually mild

SCN2A

Loss-of-function mutations

Missense mutations

KCNQ2-related epilepsies(Millichap et al., 2016)

Self-limiting epilepsy(BFNE > BFNIE, BFIE)

KCNQ2-related epilepsies(Millichap et al., 2016)

Self-limiting epilepsy(BFNE > BFNIE, BFIE)

Early-onset epileptic encephalopathy (EOEE)

Loss-of-function mutations

Missense mutations Missense mutations with dominant-negative effect

SCN2A-related disorders (Sanders et al., 2018)

Lauxmann et al., 2013

PRRT2 function (Valente et al. 2016)

A key component

of the vesicular

release of Ca2+-

dependent

neurotransmetters

• Generalized seizures often precipitated by fever (> 6 years)

• Absence, myoclonic, atonic, or partial seizures

• Variable severity

• Mendelian forms = 20%. Missense mutations of:– SCN1A (Escayg et al., 2000)

– SCN1B (Wallace et al., 1998)

– GABRG2 (Baulac et al., 2001)

– STX1B (Schubert et al. 2014).

Helbig et al., 2008

Genetic Epilepsy with Febrile Seizures +(GEFS+) (Scheffer and Berkovic, 1997)

Dravet syndrome(Dravet et al., 1992)

• Onset < 1 year

• Seizures often triggered by fever

• Prolonged seizures, status epilepticus

• Drug refractory

• Progressive motor and cognitive delay, ataxia

➢Loss-of-function heterozygous de novo mutations of SCN1A in 80% of patients (Sugawara et al., 2002)

The unified loss-of-function hypothesis for Nav1.1 genetic epilepsies (Catteral et al., 2010)

Nav1.1 expressed in GABAergicinhibitoryneurons(including

Purkinje cells)

SCN1A mutations

Clinical continuum

Dravet

CDKL5 encephalopathy (Kalscheuer et al., 2003)

History of epilepsy genetics(Helbig et al., 2016)

Molecular cytogenetics(array-CGH)

Array comparative genomic hybridization (array CGH)

PERTE

GAIN

Copy-Number Variations (CNV) = deletion(loss) or duplications (gain) > 1 kb

CNVs and epilepsy

1. Rare microdeletion syndromes:

– Angelman, del 1p36…

– Many other very rare ones

2. Recurrent CNVs associated with idiopathic epilepsies

3. CNVs that led to gene identification: STXBP1, PCDH19, GRIN2A…

•15q11.2 (de Kovel et al.,

2010)

•15q13.3 (Helbig et al.,

2009; Dibbens et al., Genet 2009)

•16p13.11 (de Kovel et al.,

2010; Heinzen et al., 2010)

Found in 3% of IGE

CNVs and idiopathic generalized epilepsy

Recurrent CNVs in IGE

• Female, 2 years: absence epilepsy with falls -> remission (stop valproate)

• 6 years: childhood absence epilepsy -> remission (stop valproate)• 13 years: myoclonia in the morning, 2 TCGS, no cognitive

impairment• No family history of epilepsy

Phenotypical variability associated with the recurrent 15q13.3 deletion

Intellectual deficiency, autism, generalized

epilepsy(0.3% patients,

0% controls)

Schizophrenia(0.2% patients,

0,01% controls)

Generalized epilepsy

(1% patients, <0,02%

controls)

Odds ratio : 68 [29 – 181]

Often inherited from an unaffected parent

= risk factor

15q13.3

Two major categories of genetic factors

Strong influence of a major gene

Mendelian epilepsies

--------

Mutation = high risk of disease

Two major categories of genetic factors

Strong influence of a major gene

Mendelian epilepsies

--------

Mutation = high risk of disease

Limited influence of a given gene

Multifactorial epilepsies

--------

Risk factors, neither necessary nor sufficient

• Mendelian inheritance rare (< 5%) -> polygenic ?

• Association studies in common epilepsies (IGE, FNLE) :

– Candidate genes or genome-wide asociation studies

– Non reproductible results: false positive, underpowered ?

• Large cohort studies :

– Epi4K/EPGP. Lancet neurol 2017: enrichment in ultrarare variants of some known genes (SCN1A, KCNQ2...)

– May et al. Lancet Neurol 2018: Enrichment in rare variants in GABAr genes

– EPi25K : ongoing

Genetic basis for common epilepsies ?

CNVs and epilepsy

1. Rare microdeletion syndromes:

– Angelman, del 1p36…

– Many other very rare ones

2. Recurrent CNVs associated with idiopathic epilepsies

3. CNVs that led to gene identification: STXBP1, PCDH19, GRIN2A…

PCDH19 in fever-sensitive epilepsy restricted to females

➢ Female-restricted epilepsy and mental retardation (Dibbens et al., 2008)

➢ Dravet-like syndrome mainly affecting females (Depienne et al., 2009)

PCDH19 and cell interference

29

Depienne et al., 2009Pederick et al., 2018, Neuron 97, 59–66• Interactions between PCDH19

andother PCDH drive the affinity for cell cell adhesion

• PCDH19- and PCDH19+ cells do not mix during cortical development

STXBP1 and EOEE (Saitsu et al., 2008)

• de novo 2.0-Mb microdeletion at 9q33.3-q34.11

• Targetted sequencing in a cohort of patients with EOEE

• 4 patients with de novomissense mutation

STXBP1 encephalopathy

• De novo mutations of STXBP1 = frequent cause of:

– EOEE with or without suppression-burst

– Infantile spasms/West, Lennox-Gastaut

• Moderate to severe intellectual disability

• Behavior disorders, autistic features

• Movement disorders: ataxia, dyskinesia,choreoathetosis

Deletions of 16p13 including GRIN2A in patients with intellectual disability, various dysmorphic features, and seizure disorders of the Rolandic region

(Reutlingen et al., Epilepsia 2010).

Microdeletions involving GRIN2A

Lesca et al., 2013

GRIN2A and epilepsia-aphasia(Lesca et al., 2013; Carvill et al., 2013; Lemke e al., 2013)

NTD = N-terminal domain, S1-2 = ligand binding sites, CTD = C-terminal domain,

LBD = ligand-binding domain

Subunit 2A of the glutamate

NMDA receptor

GRIN2A-related disorders: genotype and functional consequence predict phenotype (Strehlow et al., 2019)

Truncating variants

Missense variants

Massive parrarelsequencing era


Massive parrarelsequencing era


Epileptic encephalopathies

> 100 genes

Massive parallel sequencing(Next-generation sequencing)

37

Trio-based exome

sequencing(264 trios):

de novo mutations

2013

Trio-based exome

sequencing(264 trios):

de novo mutations

2013

SCN8A developmental and epileptic encephalopathy(Gardella et al., 2018)

Gain of function (Meisler et al., 2016)

• Median age at onset : 4 months

• Prolonged focal seizures,

cyanosis, vegetative semiology

followed by clonias

• Developmental slowing,

pyramidal/extrapyramidal signs,

movement disorders, cortical

blindness

• EEG: background deterioration,

epileptiform abnormalities

• Sodium blockers more efficient

SCN8A-related EE: two modes of onset(Denis et al., 2019)

Sudden

• Onset < 6 months

• Frequent seizures: tonic seizures or spasms

• Normal inter-ictal EEG (no supression burst)

• Evolve to GTCS and tonic seizures

Progressive

• Progressive onset or unclear

• Rare and subltle seizures: jerks, myoclonia or tremor

• Normal interictal EEG at onset

• Developmental slowing or arrest

Benign infantile seizures and paroxysmal dyskinesia caused by an SCN8A mutation

(Gardella et al., 2016)

• Tonic or GTCS

• May persist >2y

• Normal psychomotor development

• Drug-sensitive or dependant

Spectrum of SCN8A related epilepsy

➢ Efficiency of sodium blockers ?

Severe early onset DEE, high

mortality

Mild phenotype, seizures in

childhood normal cognition

Moderate DEE, often drug-

resistant seizures

Treatable seizures, mild ID

Loss of function

Gain of function

Adapted from Johannesen et al., 2019

Genes involves in both mild and severe epilepsy phenotypes

Gene Mild phenotype Severe phenotype

SCN1A GEFS+ Dravet

SCN1B GEFS+ Dravet (homozygous variants)

SCN2A Benign Familial neonatal-infantile Epilepsy EOEE

SCN8A Benign familial infantile epilepsy and paroxysmal choreoathetosis

EOEE

KCNQ2 Benign familial neonatal epilepsy EOEE

SLC2A1 Refractory generalized or focal epilepsy (early absence epilepsy)

De Vivo

GABRA1 Idiopathic generalized epilepsy EOEE

GABRG2 GEFS+ EOEE

GRIN2A Epilepsy-aphasia syndrome EOEE

Modified from Helbig and Abou Tayoum, 2016

Genetic heterogeneity in epileptic syndromes


15-20% with exome sequencing!


KCNT1 and epileptic encephalopathies

• 50% of patients with migrating partial seizures (Barcia et al., 2012)

• Ohtahara, West syndrome, unclassifiesEOEE (Ohba et al., 2015)

• Leukoencephalopathy and severe epilepsy (Vanderver et al., 2014)

Møller et al., 2015

Delineation of new epileptic syndromes

• Rare disorders with few patients in each center

• Initial description in a few patients on a rather biased manner

• Genetic findings as the common denominator

• Improve delineating :

– The electro-clinical profile(s) relateto a given gene

– Some novel electro-clinical syndromes

• Towards a gene centered classification of the epilepsies ?

SYNGAP1-related developmental encephalopathy (Mignot et al., 2016)

• Neurodevelopmental delay preceding seizure onset

• Hypotonia and unstable gait

• Intellectual disability with poor or absent language

• Autistic features in 50%

• Atonic or myoclonic seizures, absences, eyelid myoclonia

Weldon et al. 2018

• First publications:– Lennox-Gastaut (Allen et

al., 2013)

– Myoclonic epilepsy sensitive to fever (Dravet-like) (Suls et al., 2013)

Lamar and Carvill 2018

CHD2 developmental and epiletic encephalopathy

• First publications:– Lennox-Gastaut (Allen et

al., 2013)

– Myoclonic epilepsy sensitive to fever (Dravet-like) (Suls et al., 2013)

• Emerging phenotype: – Febrile seizures– Absences, myoclonias,

tonic clonic seizures– Mild to moderate ID– Pyschotic features

Lamar and Carvill 2018

CHD2 developmental and epiletic encephalopathy

SLC6A13p25.3 microdeletion of GABA transporters SLC6A1 and SLC6A11 results in intellectual disability, epilepsy and

stereotypic behaviour (Dikow et al., 2014)

• Reuptake of GABA from the inhibitory synapses

• Mutation -> reduction of GABA synaptic signalling

SLC6A1-related DEE(Johannesen et al., 2018)

• Mild to moderate ID

• Epilepsy > 90%

• Ataxia and psychitaric troubles in 20%

• Mean age at seizure onset: 3.7y

• Atypical absences, atonic, myoclonia, TCGS

• Rythmic activity 3-4 Hz, occipital predominance

KCNA2-epileptic encephalopathies (Masnada et al. 2017)

Loss of function (dominant negative)

• Onset: 8.4 months

• Predominant focal seizures

• CTS with sleep activation

• Psychomotor stagnation







Gain of function


• Febrile seizures

• Predominant generalized seizures

• More severe epilepsy

• Cognitive impairment, movement disorders







Gain of function


• Febrile seizures

• Predominant generalized seizures

• More severe epilepsy

• Cognitive impairment, movement disorders

Gain and loss of function


• Generalized and focal seizures

• More severe developmental impairment

• Cerebellar atrophy

Function of the genes causing epileptic encephalopathies

Protein function Gene (mode of inheritence)

Ion channel

Sodium SCN1A, SCN2A, SCN8A, SCN3A

Potassium KCNQ2, KCNQ3, KCNT1, KCNA2, KCNB1, KCNMA1, KCNJ10

Calcium CACNA1A

GABA-A GABRA1, GABRB1, GABRB2, GABRB3, GABRD, GABRG2

NMDA GRIN1, GRIN2A, GRIN2B, GRIN2D

Acho CHRNA2, CHRNB2, CHRNA4

HCN HCN1

Enzyme AARS, ALDH7A1, ALG13, CDKL5, CERS1, CHD2, CPA6, DNM1, EPM2A, GNAO1, ITPA, NHLRC1, PLCB1, PNPO, PRDM8, SIK1, ST3GAL3, ST3GAL5, UBA5, WWOX

Enzyme modulator ARHGEF9, CSTB, DOCK7, TBC1D24

Transporter SLC1A2, SLC12A5, SLC13A5, SLC25A12, SLC25A22, SLC2A1, SLC6A1

Receptor FRR1SL, SCARB2

Cell adhesion molecule

PCDH19

Signal transduction FGF12, DEPDC5, NPRL2, NPRL3

Membrane trafficking GORS2, STX1B, STXBP1

Cytoskeletal protein LMNB2, SPTAN1

Nucleic acid binding EE1AFA2, GUF1 McTague et al. 2016

KCNT1 and ADNFLE(Heron et al., 2012)

• Earlier age of onset

• Mostly drug-resistant

• Frequent cognitive and psychiatric comorbidity

• Missense mutations = gain of function

• High penetrance

Familial focal epilepsy with variable foci (FFEVF) (Dibbens et al.; 2013, Ishida et al., 2013)

• Variable age of onset

• +/- cognitive and psychiatric involvement

• Intra familial varability

• Loss of function mutations in: DEPDC5, NPRL2, or NPRL3

• Low penetrance (60%)

Epilepsy and mutations of gene belonging to the GATOR1 Complex (Ricos et al., 2015)

GATOR1 = GTPase-activating protein Activity Towards RAGs complex 1)

Germline DEPDC5 mutations and lesionnal focal epilepsies

• FCD type II• Heterotopia• Megalencephaly• 2nd hit = somatic

mutation in dysplastic tissue ? (Baulac et al., 2015)

Scheffer et al., 2014

Role of Somatic mutations in focal epilepsies ?

Koh and Lee, 2018


Koh and Lee, 2018


Koh and Lee, 2018

100-800x

> 2500x

Somatic mutations in epileptic disorders

Department of medical genetics,team for molecular diagnosis of

epileptic disorders

Pediatric neurology departmentDorothée Ville

Anne-Lise PoulatIsabelle Sabatier

Maryline CarneiroLaurence Lion-François

Vincent des Portes

Pediatric epilepsy departmentJulitta de BellesciseEleni PanagiotakakiPascale Keo-KosalJoseph ToulouseKarine Ostrowsky

Alexis Arzimanoglou

Practical overview of genetics in childhood epilepsies...Genes involves in both mild and severe epilepsy phenotypes Gene Mild phenotype Severe phenotype SCN1A GEFS+ Dravet SCN1B GEFS+

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