Genotype-phenotype analysis in Epilepsy: CDKL5 deficiency disorder

Heather Olson, MD, MS

Epilepsy Genetics Program and Neonatal Neurology Program

Director, CDKL5 Center of Excellence

Division of Epilepsy and Clinical Neurophysiology, Department of Neurology

Boston Children’s Hospital

Disclosures

• Grant support from NINDS, the International Foundation for CDKL5 Research, and Manton Center

• Site PI for 2 of the clinical trials mentioned with Ovid Therapeutics and Marinus Pharmaceuticals

• Consultant for Takeda Pharmaceuticals

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Overview:

•CDKL5 Centers of Excellence and the International CDKL5 Clinical Research Network (ICCRN)

•Phenotype-genotype analysis in CDKL5 deficiency disorder

•Response to treatment for spasms in CDKL5 deficiency disorder compared to controls• Plus treatment response in epilepsy more broadly

•Clinical trials and disease modifying therapies in development

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CDKL5 Centers of Excellence: Goals

• Characterize the disorder, natural history, and genotype-phenotype correlations

•Develop treatment guidelines and standards of care

•Develop and/or validate outcome measures for clinical trials

• Collaboration with industry for clinical trials

• Collaborate with family groups to meet the needs of the community

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A child with typical CDKL5 Deficiency Disorder

• early onset refractory epilepsy (initially focal then generalized, onset 11 weeks)

• global developmental delay with regression• hypotonia• progressive microcephaly• cerebral visual impairment• somatic growth retardation • hand stereotypies• dystonia and choreoathetosis

Olson and Poduri, J of Pediatric Epilepsy, 2012

EEG at 2 months:

LEFT TEMPORAL SPIKES IN SLEEP

EEG at 2 months:

LEFT TEMPORAL SPIKE IN WAKING, OTHERWISE NORMAL

EEG at 22 months:

MODIFIED HYPSARRHYTHMIA

EEG at 22 months:CLUSTER OF 3 SPASMS

EEG at 2 ½ years:SLOW, FREQUENT MULTIFOCAL EPILEPTIFORM ACTIVITY

EEG at 3 years 8 months, in waking:

CDKL5 Deficiency DisorderCommon clinical characteristics Proposed minimal diagnostic criteria

Epilepsy, early onset and refractory

Severe global developmental delay

Intellectual disability

Hypotonia

Cortical visual impairment

Sleep disturbance

Dyskinetic movements

Autonomic and breathing

disturbances

GI disturbances (reflux,

constipation)

Dysphagia

A pathogenic or likely pathogenic

variant in the CDKL5 gene

Motor and cognitive

developmental delays

Epilepsy with onset in the first year

of life

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Olson et al. Pediatric Neurology, 2019

1 13 297 905

ATP-binding site (aa 19-43)

S/T kinase active site(aa 131-143)

Thr-Glu-Tyr motif (aa 169-171)

Nuclear LocalizationSignal 1 (aa 312-315)

Nuclear Localization Signal 2 (aa 784-789)

Nuclear Export Signal(aa 836-845)

Group A

Group B

Group C Group D

Missense VariantFrameshift/Truncation VariantChromosomal Deletion/Deletion 5’ UTR

6 w/ Xp22.13

Del

Splice Variant

Group A: No functional protein (truncations before aa 172 and whole gene deletions)Group B: Missense/in-frame variants within kinase domainGroup C: Truncations from aa 172 to aa 781 inclusiveGroup D: Truncations after aa 781

Boston, Colorado, and Cleveland Children’s CDKL5 Centers of Excellence

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Olson et al, Pediatric Neurology, 2019Credit Sumaiya Iqbal and Dennis Lal

CDKL5 protein transcripts

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hCDKL5_1 is the most abundant in brainhCDKL5_2, _3, and _4 widely expressed but less abundanthCDKL5_5 only expressed in testes

Hector et al. PLOS one. 2016

Table 1 uses hg38

Original image reference: Hector et al. 2016 “Characterization of CDKL5 Transcript Isoforms in Human and Mouse”

CDKL5 Exon 1 Deletions in our cohort, Exon 1 is non-coding

Hg38 CoordinatesPatient 1:chrX:18403771-18454103Patient 2: chrX:18424145-18430358Patient 3: chrX:18426282-18428636

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1

Genotype-phenotype correlations within CDKL5 Deficiency Disorder•Missense variants in the ATP binding site – milder

clinical presentation (Bahi-Buisson et al. Am J Med Genet A 2012; Olson et al. Pediatric Neurology 2019)

• Late truncating variants – better gross motor skills, hand function and communication skills (Fehr et al. J NeurodevDisord 2015; Fehr et al. Am J Med Genet A 2016)

•Truncating variants amino acid 172-781 - lower seizure frequency compared to earlier truncations (no functional protein) (Fehr et al., Neurology 2016)

•Mosaicism – broader phenotypic spectrum, not specifically evaluated (Olson et al. Pediatric Neurology 2019)

•Sex - ~4:1 females: males, males reported as more severe though Centers of Excellence data suggests they are similar (Olson et al. Pediatric Neurology 2019, Demarest et al. Epilepsia2019)

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Genetic diagnosis in 106 patients, CDKL5 included in CDD cohort

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Phenotype of CDD compared to acontrol cohort from Boston Children’s Hospital experience,

epilepsy onset <1 year 2012 - 2019: N=105

Clinical features

CDKL5

Deficiency

Disorder (CDD)

Other infantile

onset genetic

epilepsy

P-Value (Chi-square

or Fisher's exact

test)

N = 42 N = 105

Sex, Female

Epilepsy type

33 (78.57%) 48 (45.71%) 0.0004

<0.0001

Focal 4 (9.76%) 44 (44.90%)

Generalized/Mixed 37 (90.24%) 54 (55.10%)

Treatment resistant

epilepsy39 (95.12%) 75 (72.12%) 0.002

Specific seizure patterns

Seizures with multiple

phases24 (57.14%) 6 (5.88%) <0.0001

Epileptic spasms 32 (76.19%) 29 (27.62%) <0.0001

Seizure Types

Generalized motor 38 (90.48%) 50 (48.54%) <0.001

Generalized non-motor 1 (2.50%) 14 (13.46%) 0.07

Focal motor 30 (73.17%) 72 (69.23%) 0.69

Focal non-motor 8 (20.51%) 39 (37.50%) 0.07

History of status

epilepticus

6 (14.68%) 32 (30.77%) 0.06

Defined electroclinical

syndrome

4 (9.52%) 37 (35.58%) 0.001

EEG encephalopathy

pattern31 (79.49%) 71 (68.93%) 0.30 19

Seizure types

• Complex seizure semiology with multiple phases per seizure is common (57% by COE experience, Demarest et al 2019)• Hypermotor-tonic-spasms sequence (Klein et al. Neurology 2011)

• Tonic-vibratory contraction spasms repetitive distal myoclonic jerks (Melani et al. 2011)

• Tonic-clonic-spasms (Melikishvili et al. Epilepsy and Behavior 2019)

• Other mixed motor patterns (Olson et al. Pediatric Neurology 2019, Demarest et al. Epilepsia 2019)

• Autonomic features are also common (pupillary dilation, facial flushing, irregular respirations, apneas or hyperventilation) (Olson et al. Pediatric Neurology 2019)

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Clinical featuresCDKL5 Deficiency

Disorder (CDD)

Other infantile

onset genetic

epilepsy

P-Value (Chi-square or

Fisher's exact test)

N = 42 N = 105

Global developmental

delay40 (97.56) 84 (80.77) 0.01

Developmental regression 22 (52.38%) 32 (31.07%) 0.02

Movement disorder 4 (9.52%) 19 (18.27%) 0.22

Cortical visual impairment 27 (97.37%) 30 (29.70%) < 0.001

Brain malformation 0 (0%) 12 (11.54%) 0.02

Dysmorphic features 7 (16.67%) 13 (12.38%) 0.59

Stereotypies 21 (50.0%) 11 (10.68%) <0.001

Abnormal muscle tone

Head size

Normal

Microcephaly

Macrocephaly

38 (90.48%)

32 (80.00%)

8 (20.00%)

0 (0.00%)

70 (66.67%)

82 (78.10%)

20 (19.05%)

3 (2.86%)

0.003

0.56

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Spasms and electroclinical syndromes

• Individuals with CDD were:• more likely to develop epileptic spasms (76% compared to

28%)• more likely to have hypsarrythmia (36% compared to 12%)• more likely to have regression (52% compared to 31%)

• West Syndrome and Lennox-Gastaut syndrome, however, were present at similar rates in CDD and other infantile genetic epilepsies (7% compared to 4% and 5% compared to 2% respectively)

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Spasms treatment in CDD

• Evaluated IS onset 2 months to 2 years (2012 to 2019) from 2 cohorts: patients with CDD seen in the CDKL5 Centers of Excellence and patients from the National Infantile Spasms Consortium (NISC) database• Excluded Tuberous Sclerosis Complex, Trisomy 21 or

unknown etiology with normal development

• Compared clinical response (spasm freedom) at 14 days and 3 months for ACTH, prednisolone, vigabatrin, and ketogenic diet

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Spasms treatment response in CDD compared to controls

Treatment CDD, N (%)

treated

Controls,

N (%)

treated

CDD 14

day

response

Control 14

day

response

CDD 3

month

response

Control 3

month

response

ACTH 17 (38%) 225 (60%) 4 (23% ) 138 (63%) 0/8 (0%) 128/217

(59%)

Prednisolone 17 (40%) 111 (30%) 2 (12%) 51 (53%) 0/6 (0%) 45/84 (54%)

Vigabatrin 30 (67%) 197 (53%) 7 (27%) 78 (42%) 2/19 (11%) 78/184

(42%)

CDD, N (%)

treated

Controls,

N (%)

treated

CDD 1

month

response

Control 1

month

response

CDD 3

month

response

Control 3

month

response

Ketogenic

diet

24 (53%) 51 (14%) 4/20 (20%) 23/27 (19%) 2/12 (17%) 15/40 (38%)

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Epilepsy treatment response

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Muller et al, European Journal of Pediatric Neurology 2016

Exacerbation of seizures with at least one anti-seizure medication in 31% of individuals; most often with carbamazepine (4/15).

Epilepsy treatment response

• In the Boston Children’s Hospital COE, > 50% reduction in seizures types (excluding epileptic spasms) in more than one individual occurred with the following anti-seizure medications (Olson et al. Pediatr Neurol, 2019): • phenobarbital• clobazam• topiramate• rufinamide• valproic acid

• A study of caregiver perceptions of treatment by survey (Amin et al.

Hippokratia 2017): subjective efficacy (not further defined) in more than 2 individuals to vigabatrin (12/23), clobazam (6/14), sodium valproate (5/27), and levetiracetam (3/27).

• One case series -response to vigabatrin + zonisamide for tonic-clonic-spasms in 5 patients (Melikishivili et al. Epilepsy and Behavior, 2019)

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Ketogenic diet, published data

• International CDKL5 Disorder Database (Lim et al. Epilepsia2017): • Reductions in seizure frequency in 61/104 (58.7%)• Treatment duration median 17 months

• Korean cohort evaluating response to ketogenic diet by genotype (Ko et al., Front. Neurol., 2018) • 0/10 responders (>90% seizure reduction) in the CDKL5

Deficiency disorder cohort

27www.epilepsy .com

Ketogenic diet, the Boston Children’s Hospital experience

•BCH Center of Excellence:• 22/41 had a trial of ketogenic or modified Atkins diet• 11 >50% reduction and 3 <50% reduction in seizure frequency

• 9 of 14 with response had improved alertness and development

• Duration of efficacy 5 months to 5 years• Side effects:

• Hypoglycemia (4)• Acidosis (4)• Lethargy (4)• Frequent infections (1)• GI issues (7)• Hyperuricemia/hypercalcemia (1)• Kidney stone (1)

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www.epilepsy .com

Vagal Nerve stimulation

• International CDKL5 Disorder Database (Lim et al. Epilepsy Res, 2018): 17% of 220 individuals had a VNS implanted, of whom 69% of parents reported reduced seizure frequency.

• Centers of Excellence: Improvement in 5 of 6 patients at Boston Children’s Hospital

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www.epilepsy.com

Experimental treatment approaches in CDD

• Clinical trials

• Ganaxolone, a neurosteroid – Phase 3 double blind placebo controlled trial complete (Marinus pharmaceuticals, NCT03572933), results pending

• Soticestat (TAK-935), a cholesterol 24-hydroxylase inhibitor modulating the NMDA pathway – Phase 2 study (ARCADE study, Ovid Therapeutics, NCT03694275), results pending

• Ataluren, promotor of read-through of premature stop codons - Phase 2 study (NYU Langone Health, PTC therapeutics, NCT02758626), results pending

• Fenfluramine, a serotonergic mediation – Phase 2 study (NYU Langone Health, NCT03861871), recruiting

• Disease modifying approaches such as gene therapy, gene editing, and anti-sense oligonucleotide approaches are in development

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CDKL5 Deficiency Disorder, key findings:

• Distinguishing phenotypic features include:• Female predominance but seen in males also• Highly refractory epilepsy with spasms and seizures with

multiple motor phases• High rate of cortical visual impairment • Hypotonia

• Infantile spasms response is much lower for first line treatments compared to a control cohort of patients with spasms, possibly better response to ketogenic diet

• We hope for disease modifying therapies in the future

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Thank you!• Annapurna Poduri and the Epilepsy Genetics Team

• Christelle Achkar

• Christopher Yuskaitis

• Beth Sheidley

• Lacey Smith

• Sonal Mahida

• Abbe Lai

• Emma Sexton

• Devon Knight

• Mark LaCoursiere

• Hyunyong Koh

• Barbara Robens

• Laura Turner

• Chris McGraw

• Ikhianosen Ukhuedoba

• CDKL5 research team

• Lindsay Swanson

• Jamie Love-Nichols

• Caitlin Greene

• Carolyn Daniels

• Grace Bazin

• Fellows

• Translational/basic research collaborations:

• Michela Fagiolini, BCH

• Timothy Yu and team, BCH

• Mustafa Sahin, Alessia Dinardo and lab, BCH

• Human Neuron Core: Liz Buttermore, Ivy Chen

• Jurriaan Peters, BCH

• Charles Nelson, BCH

• Dennis Lal, PhD, Cleveland Clinic and Broad Institute

• Sumaiya Iqbal, Broad Institute

• Department and Division leadership:

• Scott Pomeroy, Phillip Pearl, Clifford Woolf

Patients and families!

Manton Center for Orphan Disease Research

Eleanor and Miles Shore Fellowship, HMS

heather.olson@childrens.harvard.edu