Dissecting the genetic basis of focal cortical dysplasia: a large cohort study
Open accessAbstract
Genetic malformations of cortical development (MCDs), such as mild MCDs (mMCD), focal cortical dysplasia (FCD), and hemimegalencephaly (HME), are major causes of severe pediatric refractory epilepsies subjected to neurosurgery. FCD2 are characterized by neuropathological hallmarks that include enlarged dysmorphic neurons (DNs) and balloon cells (BCs). Here, we provide a comprehensive assessment of the contribution of germline and somatic variants in a large cohort of surgical MCD cases. We enrolled in a monocentric study 80 children with drug-resistant epilepsy and a postsurgical neuropathological diagnosis of mMCD, FCD1, FCD2, or HME. We performed targeted gene sequencing ( ≥ 2000X read depth) on matched blood-brain samples to search for low-allele frequency variants in mTOR pathway and FCD genes. We were able to elucidate 29% of mMCD/FCD1 patients and 63% of FCD2/HME patients. Somatic loss-of-function variants in the N-glycosylation pathway-associated SLC35A2 gene were found in mMCD/FCD1 cases. Somatic gain-of-function variants in MTOR and its activators (AKT3, PIK3CA, RHEB), as well as germline, somatic and two-hit loss-of-function variants in its repressors (DEPDC5, TSC1, TSC2) were found exclusively in FCD2/HME cases. We show that panel-negative FCD2 cases display strong pS6-immunostaining, stressing that all FCD2 are mTORopathies. Analysis of microdissected cells demonstrated that DNs and BCs carry the pathogenic variants. We further observed a correlation between the density of pathological cells and the variant-detection likelihood. Single-cell microdissection followed by sequencing of enriched pools of DNs unveiled a somatic second-hit loss-of-heterozygosity in a DEPDC5 germline case. In conclusion, this study indicates that mMCD/FCD1 and FCD2/HME are two distinct genetic entities: while all FCD2/HME are mosaic mTORopathies, mMCD/FCD1 are not caused by mTOR-pathway-hyperactivating variants, and ~ 30% of the cases are related to glycosylation defects. We provide a framework for efficient genetic testing in FCD/HME, linking neuropathology to genetic findings and emphasizing the usefulness of molecular evaluation in the pediatric epileptic neurosurgical population.
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Somatic mutations in mTOR pathway regulators are often found in focal cortical dysplasia type II.
“In addition, somatic mutations in mTOR pathway regulators are often found in focal cortical dysplasia type II, which has overlapping histological and clinical features with TSC24,25.”
From mTORC1 drives cell-autonomous astrocyte reactivity in tuberous sclerosis (2026) · cites this paper as [25]
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Self-citationThe paradox of cancer genes in non-malignant conditions: implications for precision medicine
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Non–Cell Autonomous Epileptogenesis in Focal Cortical Dysplasia
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Precision Therapy for Epilepsy Related to Brain Malformations
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Self-citationAcute knockdown of Depdc5 leads to synaptic defects in mTOR-related epileptogenesis.
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Genome sequencing of 320 Chinese children with epilepsy: a clinical and molecular study
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Cardiac Investigations in Sudden Unexpected Death in DEPDC5 ‐Related Epilepsy
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Large-scale neurophysiology and single-cell profiling in human neuroscience
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mTOR pathway somatic variants and the molecular pathogenesis of hemimegalencephaly
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Ultra‐Low Level Somatic Mutations and Structural Variations in Focal Cortical Dysplasia Type II
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Is Focal Cortical Dysplasia/Epilepsy Caused by Somatic MTOR Mutations Always a Unilateral Disorder?
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Human embryonic genetic mosaicism and its effects on development and disease
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The role of somatic mosaicism in brain disease
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A two-field computational model couples cellular brain development with cortical folding
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Everolimus precision therapy for the GATOR1 ‐related epilepsies: A case series
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Somatic variants in new candidate genes identified in focal cortical dysplasia type II
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Disorders Caused by Genetic Mosaicism
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Low-Level Brain Somatic Mutations Are Implicated in Schizophrenia
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Networks Underlie Temporal Onset of Dysplasia‐Related Epilepsy: A MELD Study
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Targeted suppression of mTORC2 reduces seizures across models of epilepsy
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Current Review in Basic Science: Animal Models of Focal Cortical Dysplasia and Epilepsy
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Evidence for a Dual-Pathway, 2-Hit Genetic Model for Focal Cortical Dysplasia and Epilepsy
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Defective lipid signalling caused by mutations inPIK3C2Bunderlies focal epilepsy
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Gene Editing and Modulation: the Holy Grail for the Genetic Epilepsies?
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Molecular diagnostics in drug‐resistant focal epilepsy define new disease entities
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Loss of Slc35a2 alters development of the mouse cerebral cortex
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- Authors
- Baldassari, S., Ribierre, T., Marsan, E., Adle-Biassette, H., Ferrand-Sorbets, S., Bulteau, C., Dorison, N., Fohlen, M., Polivka, M., Weckhuysen, S., Dorfmüller, G., Chipaux, M., & Baulac, S.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Hôpital Rothschild (FR)
- Hôpital Lariboisière (FR)
- Corresponding author
- Baulac, Stéphanie
- ORCID
- Venue
- Acta Neuropathologica
- Published
- 2019-08-23
- Volume
- 138
- Issue
- 6
- Pages
- 885-900
- ISSN
- 0001-6322 (ISSN-L)
- 1432-0533
- PMC
- PMC6851393
- OpenAlex
- W2969667716
- Cited by
- 356
- References
- 48
- Citations by year
- 2026: 29 · 2025: 49 · 2024: 69 · 2023: 61 · 2022: 48 · 2021: 62 · 2020: 33 · 2019: 3 · 2018: 1
- FWCI
- 29.08
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Acta Neuropathologica (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- Funders
- European Research Council (No682345)
- Topics
- Health Sciences › Medicine › Psychiatry and Mental health › Epilepsy research and treatment
- Health Sciences › Medicine › Physiology › Tuberous Sclerosis Complex Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Keywords
- focal cortical dysplasia, hemimegalencephaly, drug-resistant epilepsy, mTOR signaling, mTORopathies, SLC35A2, N-glycosylation defects, DEPDC5, TSC1, TSC2, loss-of-function mutations, balloon cells, dysmorphic neurons, genetic testing, pS6
- MeSH terms
- Adolescent, Brain, Child, Child, Preschool, Epilepsy, Female, Humans, Infant, Male, Mutation, Neurons, Cohort Studies, Malformations of Cortical Development, Hemimegalencephaly
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