Brain somatic mutations in MTOR cause focal cortical dysplasia type II leading to intractable epilepsy

Functional verification and allele-specific silencing of a novel AKT3 variant that causes megalencephaly, polymicrogyria and intractable epilepsy

AKT3, a key component of the PI3K-AKT-MTOR pathway, is highly expressed in the brain, and its activating variants cause megalencephaly and cortical malformations. In this study, we functionally verified a novel missense AKT3 variant (p.Q78R) identified in a patient with extreme megalencephaly and intractable epilepsy. We transiently transfected HEK-293T cells with the AKTWT or AKT3Q78R and observed a significant increase of phospho-S6, a marker of mTOR complex 1 (mTORC1) activity, in AKT3Q78R transfected cells. Furthermore, considering its application in epilepsy treatment research, we identified a small interfering RNA (siRNA) capable of reducing the mRNA levels of AKTQ78R without affecting the expression levels of AKT3WT. Finally, the siRNA we identified specifically suppressed the AKT3Q78R-mediated mTORC1 activity, suggesting that this allele-specific siRNA approach holds promise for ameliorating the pathological condition.

Dysregulation of Myelination in Focal Cortical Dysplasia Type II of the Human Frontal Lobe

Focal cortical dysplasias (FCDs) are local malformations of the human neocortex and a leading cause of intractable epilepsy. FCDs are classified into different subtypes including FCD IIa and IIb, characterized by a blurred gray-white matter boundary or a transmantle sign indicating abnormal white matter myelination. Recently, we have shown that myelination is also compromised in the gray matter of FCD IIa of the temporal lobe. Since myelination is key for brain function, which is imbalanced in epilepsy, in the current study, we investigated myelination in the gray matter of FCD IIa and IIb from the frontal lobe on the morphological, ultrastructural, and transcriptional level. We found that FCD IIa presents with an ordinary radial myelin fiber pattern, but with a reduced thickness of myelin sheaths of 500-1000 nm thick axons in comparison to FCD IIb and with an attenuation of the myelin synthesis machinery. In contrast, FCD IIb showed an irregular and disorganized myelination pattern covering an enlarged area in comparison to FCD IIa and controls and with increased numbers of myelinating oligodendrocytes (OLs). FCD IIb had significantly thicker myelin sheaths of large caliber axons (above 1000 nm) when compared to FCD IIa. Accordingly, FCD IIb showed a significant up-regulation of myelin-associated mRNAs in comparison to FCD IIa and enhanced binding capacities of the transcription factor MYRF to target sites in myelin-associated genes. These data indicate that FCD IIa and IIb are characterized by a differential dysregulation of myelination in the gray matter of the frontal lobe.

Alterations in dopaminergic innervation and receptors in focal cortical dysplasia

Focal cortical dysplasia (FCD) type 2 is the most common malformation of cortical development associated with pharmaco-resistant focal epilepsy and frequently located in the frontal cortex. Neuropathological hallmarks comprise abnormal cortical layering and enlarged, dysmorphic neuronal elements. Fundamentally altered local neuronal activity has been reported in human FCD type 2 epilepsy surgical biopsies. Of note, FCD type 2 emerges during brain development and forms complex connectivity architectures with surrounding neuronal networks. Local cortical microcircuits, particularly in frontal localization, are extensively modulated by monoaminergic axonal projections originating from the brainstem. Previous analysis of monoaminergic modulatory inputs in human FCD type 2 biopsies suggested altered density and distribution of these monoaminergic axons; however, a systematic investigation is still pending. Here, we perform a comprehensive analysis of dopaminergic (DA) innervation, in human FCD type 2 biopsies and in the medial prefrontal cortex (mPFC) of an FCD type 2 mouse model [mechanistic target of rapamyin (mTOR) hyperactivation model] during adolescent and adult stages. In addition, we analyse the expression of dopamine receptor transcripts via multiplex fluorescent RNA in situ hybridization in human specimens and the mPFC of this mouse model. In the mTOR hyperactivation mouse model, we observe a transient alteration of DA innervation density during adolescence and a trend towards decreased innervation in adulthood. In human FCD type 2 areas, the overall DA innervation density is decreased in adult patients compared with control areas from these patients. Moreover, the DA innervation shows an altered lamination pattern in the FCD type 2 area compared with the control area. Dopamine receptors 1 and 2 appear to be differentially expressed in the dysmorphic neurons in human samples and mTOR-mutant cells in mice compared with normally developed neurons. Intriguingly, our results suggest complex molecular and structural alterations putatively inducing impaired DA neurotransmission in FCD type 2. We hypothesize that this may have important implications for the development of these malformations and the manifestation of seizures.

Human TSC2 mutant cells exhibit aberrations in early neurodevelopment accompanied by changes in the DNA Methylome

Tuberous Sclerosis Complex (TSC) is a debilitating developmental disorder characterized by a variety of clinical manifestations. While benign tumors in the heart, lungs, kidney, and brain are all hallmarks of the disease, the most severe symptoms of TSC are often neurological, including seizures, autism, psychiatric disorders, and intellectual disabilities. TSC is caused by loss of function mutations in the TSC1 or TSC2 genes and consequent dysregulation of signaling via mechanistic Target of Rapamycin Complex 1 (mTORC1). While TSC neurological phenotypes are well-documented, it is not yet known how early in neural development TSC1/2-mutant cells diverge from the typical developmental trajectory. Another outstanding question is the contribution of homozygous-mutant cells to disease phenotypes and whether phenotypes are also present in the heterozygous-mutant populations that comprise the vast majority of cells in patients. Using TSC patient-derived isogenic induced pluripotent stem cells (iPSCs) with defined genetic changes, we observed aberrant early neurodevelopment in vitro, including misexpression of key proteins associated with lineage commitment and premature electrical activity. These alterations in differentiation were coincident with hundreds of differentially methylated DNA regions, including loci associated with key genes in neurodevelopment. Collectively, these data suggest that mutation or loss of TSC2 affects gene regulation and expression at earlier timepoints than previously appreciated, with implications for whether and how prenatal treatment should be pursued.

BRAF V600E Mutation in Ganglioglioma: Impact on Epileptogenicity and Implications for Surgical Strategy

OBJECTIVE

Gangliogliomas are commonly found pathologies in patients undergoing epilepsy surgery. While resections can be curative, seizure relapses occur. Expression of CD34 and the BRAF V600E mutation are the most common molecular biomarkers found in gangliogliomas, but their influence on seizure outcomes is unclear. We therefore reviewed our experience over two decades to better describe prognostic factors.

METHODS

We performed a retrospective chart review of all patients operated on for ganglioglioma at our institution since the year 2000. We included patients with preoperative epilepsy and a minimum follow-up of 1 year. Available tumor specimens were immunohistochemically stained for CD34 and BRAF V600E.

RESULTS

We included 62 patients with epilepsy operated for ganglioglioma. Lesionectomies were performed in 32 (51.6%), extended resections in 21 (33.9%), and partial resections in 9 cases (14.5%). Residual tumor mass on postoperative MRI was diagnosed in 21 patients (33.9%). CD34 reactivity was found in 57 patients (91.9%) and the BRAF V600E mutation was detected in 30 patients (48.4%). Patients with a BRAF V600E mutation were younger at the time of epilepsy onset (9.1 years vs. 15.2 years) and surgery (14.5 years vs. 23.7 years). Residual tumor was the largest risk factor for seizure relapses (hazard ratio 8.45) and the BRAF V600E mutation also increased this risk (hazard ratio 3.94).

CONCLUSIONS

BRAF V600E status in patients with ganglioglioma-associated epilepsy is a potential biomarker to stratify the risk for seizure relapse after surgery. BRAF V600E-positive patients might benefit from a more aggressive surgical strategy.

Detecting somatic variants in purified brain DNA obtained from surgically implanted depth electrodes in epilepsy

OBJECTIVE

Somatic variants causing epilepsy are challenging to detect, as they are only present in a subset of brain cells (e.g., mosaic), resulting in low variant allele frequencies. Traditional methods relying on surgically resected brain tissue are limited to patients undergoing brain surgery. We developed an improved protocol to detect somatic variants using DNA from stereoelectroencephalographic (SEEG) depth electrodes, enabling access to a larger patient cohort and diverse brain regions. This protocol mitigates issues of contamination and low yields by purifying neuronal nuclei using fluorescence-activated nuclei sorting (FANS).

METHODS

SEEG depth electrodes were collected upon extraction from 41 brain regions across 17 patients undergoing SEEG. Nuclei were isolated separately from depth electrodes in the affected brain regions (seizure onset zone) and the unaffected brain regions. Neuronal nuclei were isolated using FANS, and DNA was amplified using primary template amplification. Short tandem repeat (STR) analysis and postsequencing allelic imbalance assessment were used to evaluate sample integrity. High-quality amplified DNA samples from affected brain regions, patient-matched unaffected brain regions, and genomic DNA were subjected to whole exome sequencing (WES). A bioinformatic workflow was developed to reduce false positives and to accurately detect somatic variants in the affected brain region.

RESULTS

Based on DNA yield and STR analysis, 14 SEEG-derived neuronal DNA samples (seven affected and seven unaffected) across seven patients underwent WES. From the variants prioritized using our bioinformatic workflow, we chose four candidate variants in MTOR, CSDE1, KLLN, and NLE1 across four patients based on pathogenicity scores and association with phenotype. All four variants were validated using digital droplet polymerase chain reaction.

SIGNIFICANCE

Our approach enhances the reliability and applicability of SEEG-derived DNA for epilepsy, offering insights into its molecular basis, facilitating epileptogenic zone identification, and advancing precision medicine.

A missense variant in DEPDC5 resulted in abnormal morphology and increased seizure susceptibility and mortality through regulating mTOR signaling

Dishevelled, Egl-10 and Pleckstrin domain-containing 5 (DEPDC5), a key inhibitor of the mammalian/mechanistic target of rapamycin (mTOR) pathway, is frequently associated with epilepsy. However, the functional consequences of most DEPDC5 variants rely on in silico predictions and have not been experimentally confirmed.This study aimed to determine the functional consequences of a DEPDC5 variant identified in patients with epilepsy across multiple generations in a Chinese family. We identified a missense heterozygous variant (c. 2055C > A; p. Phe685Leu) in DEPDC5 in Chinese family affected by epilepsy across three generations. This variant has not been previously reported in the Chinese population. Primary neuron cultures transfected with the mutant plasmid exhibited altered subcellular localization. To explore the mechanisms of epilepsy linked to this variant, we created nervous system-specific conditional human DEPDC5 knock-in mouse using Cre-recombination under the Nestin promotor (hDEPDC5WT mice, hDEPDC5F685L mice). Compared to wildtype (WT) and hDEPDC5WT mice, hDEPDC5F685L mice exhibited histological signs of mTOR hyperactivation, enlarged neuronal soma, abnormal neurons, and heightened susceptibility to seizures and mortality. Administering rapamycin to hDEPDC5F685L mice starting two weeks after birth normalized neuronal size and mTOR activity, decreased seizure susceptibility and mortality, and showed no effects in the WT or hDEPDC5WT mice. Collectively, these results indicate that the DEPDC5 variant causes abnormal morphology and increased seizure vulnerability through modulation of mTOR signaling.

Recent progress and challenges in gene therapy for pharmacoresistant focal epilepsy

Pharmacoresistant focal epilepsy represents a major unmet need. Recent years have seen several gene therapy strategies validated mainly in rodent models of temporal lobe epilepsy, and some of these have been de-risked for clinical trials. This review considers some of the challenges in progressing from experimental models to the clinic. Among these are identifying promising promoter-transgene combinations, establishing safe and efficacious doses, achieving optimal delivery, and extrapolating across different aetiologies.

Lack of behavioural improvement with sirolimus in a patient with MTOR-related macrocephaly with pigmentary mosaicism: A new case report

Postzygotic activating MTOR variants result in neurocutaneous mosaic phenotypes including megalencephaly, focal cortical dysplasia, and pigmentary mosaicism (hypomelanosis of Ito), whereas germline activating variants cause Smith-Kinsgmore syndrome. The MTOR gene encodes the mechanistic target of rapamycin (mTOR), which is a core component of the PI3K-AKT-mTOR signaling pathway. As rapamycin downregulates the increased activity caused by the mosaic mTOR variant, it may result in improvement of clinical outcomes, as shown for refractory epilepsy in tuberous sclerosis, another genetic disease of the mTOR pathway. However, results of treatment have been reported in only three genotyped patients so far, one with pigmentary mosaicism, megalencephaly and epilepsy, and two with focal cortical dysplasia, with conflicting results. Here we report on a 12-year-old male patient with megalencephaly-pigmentary mosaicism and a mTOR mosaic gain-of-function variant (p.(Ser2413Ile)) in 23 % of affected skin cells, who received compassionate off-label sirolimus for severe behavioural disorder. Sirolimus was initiated at 1.3 mg twice a day with regular blood monitoring. After a 6-months period, no improvement was observed, neither on family environment-reported outcomes nor on neuropsychology scales, leading to treatment discontinuation. Despite physiopathological rationale, case reports have failed so far to suggest efficacy on the outcomes studied, which questioned the implementation of clinical trials.

Somatic mosaicism and interneuron involvement in mTORopathies

Somatic mutations in genes regulating mechanistic target of rapamycin (mTOR) pathway signaling can cause epilepsy, autism, and cognitive dysfunction. Research has predominantly focused on mTOR regulation of excitatory neurons in these conditions; however, dysregulated mTOR signaling among interneurons may also be critical. In this review, we discuss clinical evidence for interneuron involvement, and potential mechanisms, known and hypothetical, by which interneurons might come to directly harbor pathogenic mutations. To understand how mTOR hyperactive interneurons might drive dysfunction, we review studies in which mTOR signaling has been selectively disrupted among interneurons and interneuron progenitors in mouse model systems. Complex cellular mosaicism and dual roles for mTOR (hyper)activation in mediating disease pathogenesis and homeostatic responses raise challenging questions for effective treatment of these disorders.

A microglia clonal inflammatory disorder in Alzheimer's disease

Somatic genetic heterogeneity resulting from post-zygotic DNA mutations is widespread in human tissues and can cause diseases, however, few studies have investigated its role in neurodegenerative processes such as Alzheimer's disease (AD). Here, we report the selective enrichment of microglia clones carrying pathogenic variants, that are not present in neuronal, glia/stromal cells, or blood, from patients with AD in comparison to age-matched controls. Notably, microglia-specific AD-associated variants preferentially target the MAPK pathway, including recurrent CBL ring-domain mutations. These variants activate ERK and drive a microglia transcriptional program characterized by a strong neuro-inflammatory response, both in vitro and in patients. Although the natural history of AD-associated microglial clones is difficult to establish in humans, microglial expression of a MAPK pathway activating variant was previously shown to cause neurodegeneration in mice, suggesting that AD-associated neuroinflammatory microglial clones may contribute to the neurodegenerative process in patients.

A new perspective on drug-resistant epilepsy in children with focal cortical dysplasia type 1: From challenge to favorable outcome

OBJECTIVE

We comprehensively characterized a large pediatric cohort with focal cortical dysplasia (FCD) type 1 to expand the phenotypic spectrum and to identify predictors of postsurgical outcomes.

METHODS

We included pediatric patients with histopathological diagnosis of isolated FCD type 1 and at least 1 year of postsurgical follow-up. We systematically reanalyzed clinical, electrophysiological, and radiological features. The results of this reanalysis served as independent variables for subsequent statistical analyses of outcome predictors.

RESULTS

All children (N = 31) had drug-resistant epilepsy with varying impacts on neurodevelopment and cognition (presurgical intelligence quotient [IQ]/developmental quotient scores = 32-106). Low presurgical IQ was associated with abnormal slow background electroencephalographic (EEG) activity and disrupted sleep architecture. Scalp EEG showed predominantly multiregional and often bilateral epileptiform activity. Advanced epilepsy magnetic resonance imaging (MRI) protocols identified FCD-specific features in 74.2% of patients (23/31), 17 of whom were initially evaluated as MRI-negative. In six of eight MRI-negative cases, fluorodeoxyglucose-positron emission tomography (PET) and subtraction ictal single photon emission computed tomography coregistered to MRI helped localize the dysplastic cortex. Sixteen patients (51.6%) underwent invasive EEG. By the last follow-up (median = 5 years, interquartile range = 3.3-9 years), seizure freedom was achieved in 71% of patients (22/31), including seven of eight MRI-negative patients. Antiseizure medications were reduced in 21 patients, with complete withdrawal in six. Seizure outcome was predicted by a combination of the following descriptors: age at epilepsy onset, epilepsy duration, long-term invasive EEG, and specific MRI and PET findings.

SIGNIFICANCE

This study highlights the broad phenotypic spectrum of FCD type 1, which spans far beyond the narrow descriptions of previous studies. The applied multilayered presurgical approach helped localize the epileptogenic zone in many previously nonlesional cases, resulting in improved postsurgical seizure outcomes, which are more favorable than previously reported for FCD type 1 patients.

Neuropathology of focal epilepsy: the promise of artificial intelligence and digital Neuropathology 3.0

Focal lesions of the human neocortex often cause drug-resistant epilepsy, yet ​surgical resection of the epileptogenic region has been proven as a successful strategy to control seizures in a carefully selected patient cohort. Continuous efforts to study neurosurgically resected brain samples at the microscopic level, i.e., Neuropathology 1.0, unravelled a comprehensive description of the spectrum of underlying aetiologies, e.g., hippocampal sclerosis, congenital brain tumours or cortical malformations as the three most common aetiologies representing almost 80% of the entire lesional landscape. Human brain tissue was also instrumental to discover underlying molecular pathways and common somatic variants, e.g., MTOR, DEPDC5, SLC35A2, BRAF or PTPN11, that helped us to define specific phenotype-genotype associations, thereby promoting novel targets for medical treatment, i.e., Neuropathology 2.0. The increasing gap in accessing necessary resources to perform such studies around the world could be bridged, however, when introducing artificial intelligence (AI)-based algorithms to classify epileptogenic brain lesions on digital slide scans obtained from routine haematoxylin and eosin-stained, formalin-fixed paraffin-embedded tissue sections. This may also provide an advanced prediction of the lesion's phenotype-genotype association in the near future. Thus, digital Neuropathology 3.0 may be the promising next level of laboratory advancement in the realm of neuropathology in focal epilepsy.

Cytomegalic parvalbumin neurons in fetal cases of hemimegalencephaly

OBJECTIVE

Mutations in genes of the mTOR pathway have been identified as a major cause of hemimegalencephaly (HMG), focal cortical dysplasia type II, and tuberous sclerosis, cortical malformations associated with epilepsy. These conditions are characterized at the cellular level by increased size of pyramidal neurons that grow with dysmorphic features and in some cases by the presence of giant balloon cells. Our previous research in tuberous sclerosis has shown that parvalbumin (Pvalb) and calbindin immunoreactive cells in cortical and subcortical tuberal lesions show cytomegalic features, suggesting the involvement of GABAergic cells in mTOR-related pathologies. In the present report, we propose to deepen our understanding of the role of interneurons in mTOR-related cortical malformations by analyzing the maturation of Pvalb neurons in fetal samples of HMG.

METHODS

We performed immunohistochemical staining of cortical samples from individuals with HMG from 21 gestational weeks to 10 postnatal months. The study focused on Pvalb cells, and pS6 counterstaining was performed to assess the activation of the mTOR pathway. To investigate the pathomechanisms behind the cytomegalic features, we examined mTOR pathway gene expression in Pvalb interneurons and cortical projection neurons using a single-cell transcriptomic atlas of the human neocortex.

RESULTS

Our results revealed cytomegalic features in Pvalb interneurons, indicating abnormal development in HMG patients compared to controls. This phenotype progressively worsened over time, suggesting ongoing developmental abnormalities associated with mTOR dysregulation, which may underlie the pathology of cortical malformations in HMG. Our transcriptomic data revealed similar expression patterns of mTOR and its upstream regulators in both Pvalb and glutamatergic neurons during development, suggesting that mTOR pathway disorders may induce similar phenotypes in both cell types.

SIGNIFICANCE

The present data suggest that Pvalb interneurons are involved in the development of mTOR-related cortical dysplasia and that they may be a contributor to the clinical phenotype of these patients.

Focal cortical dysplasia type II: review of neuropathological manifestations and pathogenetic mechanisms

Focal cortical dysplasia (FCD) is an important cause of intractable epilepsy, with FCD type II (FCD II) being the most common subtype. FCD II is characterized by cortical dyslamination accompanied by dysmorphic neurons (DNs). Identifying the molecular alterations and targetable biomarkers is pivotal for developing therapies. Here, we provide a detailed description of the neuropathological manifestations of FCD II, including morphological alterations and immunophenotypic profiles, indicating that abnormal cells exhibit a diverse spectrum of mixed differentiation states. Furthermore, we summarize current research on the pathogenetic mechanisms, indicating that gene mutations, epigenetic alterations, cortical developmental protein disturbances, inflammatory processes, and extrinsic damages may lead to abnormal neuronal proliferation and migration, thereby contributing to the emergence and progression of FCD II. These findings not only enhance our understanding of the pathogenesis of FCD II but also offer new directions for clinical diagnosis and treatment. Future research should further explore the interactions among these factors and employ multidisciplinary approaches to advance our understanding of FCD II.

Chloride deregulation and GABA depolarization in MTOR-related malformations of cortical development

Focal cortical dysplasia, hemimegalencephaly and cortical tubers are paediatric epileptogenic malformations of cortical development (MCDs) frequently pharmacoresistant and mostly treated surgically by the resection of epileptic cortex. Availability of cortical resection samples has allowed significant mechanistic discoveries directly from human material. Causal brain somatic or germline mutations in the AKT/PI3K/DEPDC5/MTOR genes have been identified. GABAA-mediated paradoxical depolarization, related to altered chloride (Cl-) homeostasis, has been shown to participate to ictogenesis in human paediatric MCDs. However, the link between genomic alterations and neuronal hyperexcitability is unclear. Here, we studied the post-translational interactions between the mTOR pathway and the regulation of cation-chloride cotransporters (CCCs), KCC2 and NKCC1, that are largely responsible for controlling intracellular Cl- and, ultimately, GABAergic transmission. For this study, 35 children (25 MTORopathies and 10 pseudo-controls, diagnosed by histology plus genetic profiling) were operated for drug-resistant epilepsy. Postoperative cortical tissues were recorded on a multi-electrode array to map epileptic activities. CCC expression level and phosphorylation status of the WNK1/SPAK-OSR1 pathway was measured during basal conditions and after pharmacological modulation. Direct interactions between mTOR and WNK1 pathway components were investigated by immunoprecipitation. Membranous incorporation of MCD samples in Xenopus laevis oocytes enabled measurement of the Cl- conductance and equilibrium potential for GABA. Of the 25 clinical cases, half harboured a somatic mutation in the mTOR pathway, and pS6 expression was increased in all MCD samples. Spontaneous interictal discharges were recorded in 65% of the slices. CCC expression was altered in MCDs, with a reduced KCC2/NKCC1 ratio and decreased KCC2 membranous expression. CCC expression was regulated by the WNK1/SPAK-OSR1 kinases through direct phosphorylation of Thr906 on KCC2, which was reversed by WNK1 and SPAK antagonists (N-ethylmaleimide and staurosporine). The mSIN1 subunit of MTORC2 was found to interact with SPAK-OSR1 and WNK1. Interactions between these key epileptogenic pathways could be reversed by the mTOR-specific antagonist rapamycin, leading to a dephosphorylation of CCCs and recovery of the KCC2/NKCC1 ratio. The functional effect of such recovery was validated by the restoration of the depolarizing shift in the equilibrium potential for GABA by rapamycin, measured after incorporation of MCD membranes into X. laevis oocytes, in line with a re-establishment of normal Cl- reversal potential. Our study deciphers a protein interaction network through a phosphorylation cascade between MTOR and WNK1/SPAK-OSR1 leading to deregulation of chloride cotransporters, increased neuronal Cl- levels and GABAA dysfunction in malformations of cortical development, linking genomic defects and functional effects and paving the way to target epilepsy therapy.

ILAE genetic literacy series: Focal cortical dysplasia

Focal cortical dysplasia (FCD) is a common cause of drug-resistant focal epilepsy in children and young adults and is often surgically remediable. The genetics of FCD are increasingly understood due to the ability to perform genomic testing including deep sequencing of resected FCD tissue specimens. There is clear evidence that FCD type II occurs secondary to both germline and somatic mTOR pathway variants, while emerging literature supports the role of SLC35A2, a glycosylation gene, in mild malformation of cortical development with oligodendroglial hyperplasia and epilepsy (MOGHE). Herein, we provide a review of FCDs focusing on their clinical phenotypes, genetic basis, and management considerations when performing genetic testing in this patient group.

Personalized Human Astrocyte-Derived Region-Specific Forebrain Organoids Recapitulate Endogenous Pathological Features of Focal Cortical Dysplasia

Focal cortical dysplasia (FCD) is a highly heterogeneous neurodevelopmental malformation, the underlying mechanisms of which remain largely elusive. In this study, personalized dorsal and ventral forebrain organoids (DFOs/VFOs) are generated derived from brain astrocytes of patients with FCD type II (FCD II). The pathological features of dysmorphic neurons, balloon cells, and astrogliosis are successfully replicated in patient-derived DFOs, but not in VFOs. It is noteworthy that cardiomyocyte-like cells correlated with dysmorphic neurons are generated through the high activation of BMP and WNT signaling in some of the FCD-organoids and patient cortical tissues. Moreover, functional assessments demonstrated the occurrence of epileptiform burst firing and propagative self-assembling neuronal hyperactivity in both FCD-DFOs and VFOs. Additionally, the heterotopic cardiomyocyte-organoids demonstrated the capacity for cardiomyocyte contraction and rhythmic firing. The presence of these cardiomyocytes contributes to the hyperactivity of neural networks in cardioids-DFOs assembly. In conclusion, the personalized region-specific forebrain organoids derived from FCD patient astrocytes effectively recapitulate heterogeneous pathological features, offering a valuable platform for the development of precise therapeutic strategies.

Efficacy and safety of everolimus for patients with focal cortical dysplasia type 2

OBJECTIVE

This study aimed to evaluate the effectiveness and safety of everolimus in treating seizures associated with focal cortical dysplasia type 2 (FCD 2).

METHODS

A prospective, crossover, placebo-controlled clinical trial (ClinicalTrials.gov: NCT03198949) enrolled patients aged 4-40 years with pathologically confirmed FCD 2 and a history of ≥3 seizures per month for two out of the 3 months prior to screening. The trial included a 4-week baseline phase, two 12-week core phases, and a 29-week extension phase. Patients received everolimus or placebo in a blinded manner during core phase I, with crossover to the alternate treatment in core phase II. Everolimus dosage started at 4.5 mg/m2/day, targeting a serum level of 5-15 ng/mL. The primary outcome was the proportion of patients achieving ≥50% seizure reduction from baseline in the last month of each core phase. Safety profiles were compared between groups.

RESULTS

Between May 11, 2017, and June 19, 2020, 21 patients completed the core phases. There was no significant difference in the primary outcome between everolimus and placebo groups (24% vs. 19%, p = 0.66). The patients showed varied responses. Three patients with a pathogenic variant in the MTOR gene or no genetic abnormalities achieved seizure freedom with everolimus in the last month of the core phase, while none of the patients with variants in other genes did. Adverse events, such as mucositis or skin ulceration, were more common with everolimus (19/21 vs. 7/21, p < 0.001). All adverse events resolved without study drug withdrawal.

SIGNIFICANCE

Everolimus treatment for 12 weeks did not show overall superiority in reducing seizures compared to placebo. However, it showed promise, mostly in patients with a pathogenic variant in the MTOR gene, highlighting the need for further research into patient-specific factors influencing treatment response. The everolimus treatment was generally safe and manageable.

PLAIN LANGUAGE SUMMARY

This study tested everolimus for reducing seizures in patients with focal cortical dysplasia type 2 (FCD 2). While the drug was not more effective than a placebo for most, few patients showed better results, with some becoming seizure-free. Side effects were common but manageable. More research is needed to understand why certain patients respond better to treatment.

Somatic DNA Variants in Epilepsy Surgery Brain Samples from Patients with Lesional Epilepsy

Epilepsy affects 50 million people worldwide and is drug-resistant in approximately one-third of cases. Even when a structural lesion is identified as the epileptogenic focus, understanding the underlying genetic causes is crucial to guide both counseling and treatment decisions. Both somatic and germline DNA variants may contribute to the lesion itself and/or influence the severity of symptoms. We therefore used whole exome sequencing (WES) to search for potentially pathogenic somatic DNA variants in brain samples from children with lesional epilepsy who underwent epilepsy surgery. WES was performed on 20 paired DNA samples extracted from both lesional brain tissue and reference tissue from the same patient, such as leukocytes or fibroblasts. The paired WES data were jointly analyzed using GATK Mutect2 to identify somatic single nucleotide variants (SNVs) or insertions/deletions (InDels), which were subsequently evaluated in silico for their disease-causing potential using MutationTaster2021. We identified known pathogenic somatic variants in five patients (25%) with variant allele frequencies (VAF) ranging from 3-35% in the genes MTOR, TSC2, PIK3CA, FGFR1, and PIK3R1 as potential causes of cortical malformations or central nervous system (CNS) tumors. Depending on the VAF, we used different methods such as Sanger sequencing, allele-specific qPCR, or targeted ultra-deep sequencing (amplicon sequencing) to confirm the variant. In contrast to the usually straightforward confirmation of germline variants, the validation of somatic variants is more challenging because current methods have limitations in sensitivity, specificity, and cost-effectiveness. In our study, WES identified additional somatic variant candidates in additional genes with VAFs ranging from 0.7-7.0% that could not be validated by an orthogonal method. This highlights the importance of variant validation, especially for those with very low allele frequencies.

Iconography of abnormal non-neuronal cells in pediatric focal cortical dysplasia type IIb and tuberous sclerosis complex

Once believed to be the culprits of epileptogenic activity, the functional properties of balloon/giant cells (BC/GC), commonly found in some malformations of cortical development including focal cortical dysplasia type IIb (FCDIIb) and tuberous sclerosis complex (TSC), are beginning to be unraveled. These abnormal cells emerge during early brain development as a result of a hyperactive mTOR pathway and may express both neuronal and glial markers. A paradigm shift occurred when our group demonstrated that BC/GC in pediatric cases of FCDIIb and TSC are unable to generate action potentials and lack synaptic inputs. Hence, their role in epileptogenesis remained obscure. In this review, we provide a detailed characterization of abnormal non-neuronal cells including BC/GC, intermediate cells, and dysmorphic/reactive astrocytes found in FCDIIb and TSC cases, with special emphasis on electrophysiological and morphological assessments. Regardless of pathology, the electrophysiological properties of abnormal cells appear more glial-like, while others appear more neuronal-like. Their morphology also differs in terms of somatic size, shape, and dendritic elaboration. A common feature of these types of non-neuronal cells is their inability to generate action potentials. Thus, despite their distinct properties and etiologies, they share a common functional feature. We hypothesize that, although the exact role of abnormal non-neuronal cells in FCDIIb and TSC remains mysterious, it can be suggested that cells displaying more glial-like properties function in a similar way as astrocytes do, i.e., to buffer K+ ions and neurotransmitters, while those with more neuronal properties, may represent a metabolic burden due to high energy demands but inability to receive or transmit electric signals. In addition, due to the heterogeneity of these cells, a new classification scheme based on morphological, electrophysiological, and gene/protein expression in FCDIIb and TSC cases seems warranted.

Somatic Mosaicism in Brain Disorders

Research efforts over the past decade have defined the genetic landscape of somatic variation in the brain. Neurons accumulate somatic mutations from development through aging with potentially profound functional consequences. Recent studies have revealed the contribution of somatic mosaicism to various brain disorders including focal epilepsy, neuropsychiatric disease, and neurodegeneration. One notable finding is that the effect of somatic mosaicism on clinical outcomes can vary depending on contextual factors, such as the developmental origin of a variant or the number and type of cells affected. In this review, we highlight current knowledge regarding the role of somatic mosaicism in brain disorders and how biological context can mediate phenotypes. First, we identify the origins of brain somatic variation throughout the lifespan of an individual. Second, we explore recent discoveries that suggest somatic mosaicism contributes to various brain disorders. Finally, we discuss neuropathological associations of brain mosaicism in different biological contexts and potential clinical utility.

SLC35A2 loss of function variants affect glycomic signatures, neuronal fate, and network dynamics

SLC35A2 encodes a UDP-galactose transporter essential for glycosylation of proteins and galactosylation of lipids and glycosaminoglycans. Germline genetic SLC35A2 variants have been identified in congenital disorders of glycosylation and somatic SLC35A2 variants have been linked to intractable epilepsy associated with malformations of cortical development. However, the functional consequences of these pathogenic variants on brain development and network integrity remain elusive. In this study, we use an isogenic human induced pluripotent stem cell-derived neuron model to comprehensively interrogate the functional impact of loss of function variants in SLC35A2 through the integration of cellular and molecular biology, protein glycosylation analysis, neural network dynamics, and single cell electrophysiology. We show that loss of function variants in SLC35A2 result in disrupted glycomic signatures and precocious neurodevelopment, yielding hypoactive, asynchronous neural networks. This aberrant network activity is attributed to an inhibitory/excitatory imbalance as characterization of neural composition revealed preferential differentiation of SLC35A2 loss of function variants towards the GABAergic fate. Additionally, electrophysiological recordings of synaptic activity reveal a shift in excitatory/inhibitory balance towards increased inhibitory drive, indicating changes occurring specifically at the pre-synaptic terminal. Our study is the first to provide mechanistic insight regarding the early development and functional connectivity of SLC35A2 loss of function variant harboring human neurons, providing important groundwork for future exploration of potential therapeutic interventions.

Multimodal single-cell profiling reveals neuronal vulnerability and pathological cell states in focal cortical dysplasia

Focal cortical dysplasia (FCD) is a neurodevelopmental condition characterized by malformations of the cerebral cortex that often cause drug-resistant epilepsy. In this study, we performed multi-omics single-nuclei profiling to map the chromatin accessibility and transcriptome landscapes of FCD type II, generating a comprehensive multimodal single-nuclei dataset comprising 61,525 cells from 11 clinical samples of lesions and controls. Our findings revealed profound chromatin, transcriptomic, and cellular alterations affecting neuronal and glial cells in FCD lesions, including the selective loss of upper-layer excitatory neurons, significant expansion of oligodendrocytes and immature astrocytic populations, and a distinct neuronal subpopulation harboring dysmorphic neurons. Furthermore, we uncovered activated microglia subsets, particularly in FCD IIb cases. This comprehensive study unveils neuronal and glial cell states driving FCD development and epileptogenicity, enhancing our understanding of FCD and offering directions for targeted therapy development.

Somatic variant analysis of resected brain tissue in epilepsy surgery patients

We studied the distribution of germline and somatic variants in epilepsy surgery patients with (suspected) malformations of cortical development (MCD) who underwent surgery between 2015 and 2020 at University Medical Center Utrecht (the Netherlands) and pooled our data with four previously published cohort studies. Tissue analysis yielded a pathogenic variant in 203 of 663 (31%) combined cases. In 126 of 379 (33%) focal cortical dysplasia (FCD) type II cases and 23 of 37 (62%) hemimegalencephaly cases, a pathogenic variant was identified, mostly involving the mTOR signaling pathway. Pathogenic variants in 10 focal epilepsy genes were found in 48 of 178 (27%) FCDI/mild MCD/mMCD with oligodendroglial hyperplasia and epilepsy cases; 36 of these (75%) were SLC35A2 variants. Six of 69 (9%) patients without a histopathological lesion had a pathogenic variant in SLC35A2 (n = 5) or DEPDC5 (n = 1). A germline variant in blood DNA was confirmed in all cases with a pathogenic variant in tissue, with a variant allele frequency (VAF) of ~50%. In seven of 114 patients (6%) with a somatic variant in tissue, mosaicism in blood was detected. More than half of pathogenic somatic variants had a VAF < 5%. Further analysis of the correlation between genetic variants and surgical outcomes will improve patient counseling and may guide postoperative treatment decisions.

Identification and verification of key molecules in the epileptogenic process of focal cortical dysplasia

Focal cortical dysplasia (FCD) represents a common developmental malformation associated with drug-resistant epilepsy (DRE) among children. However, the exact molecular mechanisms behind this condition are still unclear. In our study, FCD-associated microarray data from the Gene Expression Omnibus (GEO) database were analyzed. A comprehensive series of bioinformatics analyses were conducted, including screening for differentially expressed genes (DEGs), functional enrichment analysis, weighted gene co-expression network analysis (WGCNA), and protein-protein interaction (PPI) analysis. Subsequently, a freezing lesion (FL) rat model was developed to validate expression levels of hub genes along with the molecular pathways behind FCD epileptogenicity. 320 DEGs were identified, and functional enrichment analysis revealed significant enrichment of these DEGs in "Neuroinflammatory response", "Cytokine production involved in immune response", and "Macrophage activation". Ultimately, 5 potential hub genes (CYBB, ITGAM, FCG3A, LY86, and CD86) were pinpointed. Notably, 4 hub genes (CYBB, ITGAM, FCG3A, and CD86) were validated in in vivo experiments, suggesting possible associations with neuroinflammation triggered by microglia. This underscores the tight relationship between microglia-induced neuroinflammation and the pathological progression of epileptic seizures in FCD. ITGAM, FCG3A, CD86, CYBB, and LY86 may emerge as promising candidate biomarkers, influencing diagnostic and therapeutic strategies.

Variants of TSC1 are associated with developmental and epileptic encephalopathy and focal epilepsy without tuberous sclerosis : For the China Epilepsy Gene 1.0 Project

BACKGROUND

The TSC1 gene encodes a growth inhibitory protein hamartin, which plays a crucial role in negative regulation of the activity of mTORC1 (mechanistic target of rapamycin complex 1). TSC1 has been associated with tuberous sclerosis complex (TSC). This study aims to investigate the association between TSC1 variants and common epilepsy.

METHODS

Trio-based whole-exome sequencing was performed in epilepsy patients without acquired etiologies from the China Epilepsy Gene 1.0 Project platform. The pathogenicity of the variants was evaluated according to the American College of Medical Genetics and Genomic (ACMG) guidelines.

RESULTS

Two TSC1 de novo variants, including c.1498 C > T/p.Arg500* and c.2356 C > T/p.Arg786*, were identified in two patients with developmental and epileptic encephalopathy (DEE). The patients exhibited frequent seizures and neurodevelopmental delay. Additionally, we identified two heterozygous TSC1 variants that affected four individuals with focal epilepsy from two unrelated families. The four probands did not present any typical symptom of TSC and had normal brain MRI findings. The four variants were absent in the Genome Aggregation Database (gnomAD) and were predicted to be damaging with a in silico prediction tool. Based on the ACMG guidelines, the four variants were evaluated to be "pathogenic" or "likely pathogenic". Of the patients in the China Epilepsy Gene 1.0 Project, 22 patients carried TSC1 variants and were diagnosed with TSC. The ratio of patients carrying TSC1 variants with or without TSC is about 5:1.

CONCLUSIONS

TSC1 is potentially associated with common epilepsy without tuberous sclerosis.

mTORC1 restricts TFE3 activity by auto-regulating its presence on lysosomes

To stimulate cell growth, the protein kinase complex mTORC1 requires intracellular amino acids for activation. Amino-acid sufficiency is relayed to mTORC1 by Rag GTPases on lysosomes, where growth factor signaling enhances mTORC1 activity via the GTPase Rheb. In the absence of amino acids, GATOR1 inactivates the Rags, resulting in lysosomal detachment and inactivation of mTORC1. We demonstrate that in human cells, the release of mTORC1 from lysosomes depends on its kinase activity. In accordance with a negative feedback mechanism, activated mTOR mutants display low lysosome occupancy, causing hypo-phosphorylation and nuclear localization of the lysosomal substrate TFE3. Surprisingly, mTORC1 activated by Rheb does not increase the cytoplasmic/lysosomal ratio of mTORC1, indicating the existence of mTORC1 pools with distinct substrate specificity. Dysregulation of either pool results in aberrant TFE3 activity and may explain nuclear accumulation of TFE3 in epileptogenic malformations in focal cortical dysplasia type II (FCD II) and tuberous sclerosis (TSC).

Clinical and functional studies of MTOR variants in Smith-Kingsmore syndrome reveal deficits of circadian rhythm and sleep-wake behavior

Heterozygous de novo or inherited gain-of-function mutations in the MTOR gene cause Smith-Kingsmore syndrome (SKS). SKS is a rare autosomal dominant condition, and individuals with SKS display macrocephaly/megalencephaly, developmental delay, intellectual disability, and seizures. A few dozen individuals are reported in the literature. Here, we report a cohort of 28 individuals with SKS that represent nine MTOR pathogenic variants. We conducted a detailed natural history study and found pathophysiological deficits among individuals with SKS in addition to the common neurodevelopmental symptoms. These symptoms include sleep-wake disturbance, hyperphagia, and hyperactivity, indicative of homeostatic imbalance. To characterize these variants, we developed cell models and characterized their functional consequences. We showed that these SKS variants display a range of mechanistic target of rapamycin (mTOR) activities and respond to the mTOR inhibitor, rapamycin, differently. For example, the R1480_C1483del variant we identified here and the previously known C1483F are more active than wild-type controls and less responsive to rapamycin. Further, we showed that SKS mutations dampened circadian rhythms and low-dose rapamycin improved the rhythm amplitude, suggesting that optimal mTOR activity is required for normal circadian function. As SKS is caused by gain-of-function mutations in MTOR, rapamycin was used to treat several patients. While higher doses of rapamycin caused delayed sleep-wake phase disorder in a subset of patients, optimized lower doses improved sleep. Our study expands the clinical and molecular spectrum of SKS and supports further studies for mechanism-guided treatment options to improve sleep-wake behavior and overall health.

Human embryonic genetic mosaicism and its effects on development and disease

Nearly every mammalian cell division is accompanied by a mutational event that becomes fixed in a daughter cell. When carried forward to additional cell progeny, a clone of variant cells can emerge. As a result, mammals are complex mosaics of clones that are genetically distinct from one another. Recent high-throughput sequencing studies have revealed that mosaicism is common, clone sizes often increase with age and specific variants can affect tissue function and disease development. Variants that are acquired during early embryogenesis are shared by multiple cell types and can affect numerous tissues. Within tissues, variant clones compete, which can result in their expansion or elimination. Embryonic mosaicism has clinical implications for genetic disease severity and transmission but is likely an under-recognized phenomenon. To better understand its implications for mosaic individuals, it is essential to leverage research tools that can elucidate the mechanisms by which expanded embryonic variants influence development and disease.

[(Auto)immunity in focal epilepsy: mechanisms of (auto‑)immune-inflammatory epileptogenic neurodegeneration]

OBJECTIVE

While the neuronal mechanisms of epileptic hyperexcitability (HE) have been studied in detail, recent findings suggest that extraneuronal, mainly immune-mediated inflammatory and vascular mechanisms play an important role in the development and progression of HE in epilepsy and the cognitive and behavioral comorbidities.

MATERIAL AND METHODS

Narrative review.

RESULTS

As in autoimmune (limbic) encephalitis (ALE/AIE) or Rasmussen's encephalitis (RE), the primary adaptive and innate immune responses and associated changes in the blood-brain barrier (BBB) and neurovascular unit (NVU) can cause acute cortical hyperexcitability (HE) and the development of hippocampal sclerosis (HS) and other structural cortical lesions with chronic HE. Cortical HE, which is associated with malformation of cortical development (MCD) and low-grade epilepsy-associated tumors (LEAT), for example, can be accompanied by secondary adaptive and innate immune responses and alterations in the BBB and NVU, potentially modulating the ictogenicity and epileptogenicity. These associations illustrate the influence of adaptive and innate immune mechanisms and associated changes in the BBB and NVU on cortical excitability and vice versa, suggesting a dynamic and complex interplay of these factors in the development and progression of epilepsy in general.

DISCUSSION

The described concept of a neuro-immune-vascular interaction in focal epilepsy opens up new possibilities for the pathogenetic understanding and thus also for the selective therapeutic intervention.

Polymers as Efficient Non-Viral Gene Delivery Vectors: The Role of the Chemical and Physical Architecture of Macromolecules

Gene therapy is the technique of inserting foreign genetic elements into host cells to achieve a therapeutic effect. Although gene therapy was initially formulated as a potential remedy for specific genetic problems, it currently offers solutions for many diseases with varying inheritance patterns and acquired diseases. There are two major groups of vectors for gene therapy: viral vector gene therapy and non-viral vector gene therapy. This review examines the role of a macromolecule's chemical and physical architecture in non-viral gene delivery, including their design and synthesis. Polymers can boost circulation, improve delivery, and control cargo release through various methods. The prominent examples discussed include poly-L-lysine, polyethyleneimine, comb polymers, brush polymers, and star polymers, as well as hydrogels and natural polymers and their modifications. While significant progress has been made, challenges still exist in gene stabilization, targeting specificity, and cellular uptake. Overcoming cytotoxicity, improving delivery efficiency, and utilizing natural polymers and hybrid systems are vital factors for prospects. This comprehensive review provides an illuminating overview of the field, guiding the way toward innovative non-viral-based gene delivery solutions.

Threshold of somatic mosaicism leading to brain dysfunction with focal epilepsy

Somatic mosaicism in a fraction of brain cells causes neurodevelopmental disorders, including childhood intractable epilepsy. However, the threshold for somatic mosaicism leading to brain dysfunction is unknown. In this study, we induced various mosaic burdens in focal cortical dysplasia type II (FCD II) mice, featuring mTOR somatic mosaicism and spontaneous behavioural seizures. The mosaic burdens ranged from approximately 1000 to 40 000 neurons expressing the mTOR mutant in the somatosensory or medial prefrontal cortex. Surprisingly, approximately 8000-9000 neurons expressing the MTOR mutant, extrapolated to constitute 0.08%-0.09% of total cells or roughly 0.04% of variant allele frequency in the mouse hemicortex, were sufficient to trigger epileptic seizures. The mutational burden was correlated with seizure frequency and onset, with a higher tendency for electrographic inter-ictal spikes and beta- and gamma-frequency oscillations in FCD II mice exceeding the threshold. Moreover, mutation-negative FCD II patients in deep sequencing of their bulky brain tissues revealed somatic mosaicism of the mTOR pathway genes as low as 0.07% in resected brain tissues through ultra-deep targeted sequencing (up to 20 million reads). Thus, our study suggests that extremely low levels of somatic mosaicism can contribute to brain dysfunction.

Are High-Frequency Activities Reliable Biomarkers of the FCDII Lesion?

Mouse Model of Focal Cortical Dysplasia Type II Generates a Wide Spectrum of High-Frequency Activities Chvojka J, Prochazkova N, Rehorova M, Kudlacek J, Kylarova S, Kralikova M, Buran P, Weissova R, Balastik M, Jefferys JGR, Novak O, Jiruska P. Neurobiol Dis. 2024;190:106383. Epub 2023 Dec 17. PMID: 38114051. doi: 10.1016/j.nbd.2023.106383 High-frequency oscillations (HFOs) represent an electrographic biomarker of endogenous epileptogenicity and seizure-generating tissue that proved clinically useful in presurgical planning and delineating the resection area. In the neocortex, the clinical observations on HFOs are not sufficiently supported by experimental studies stemming from a lack of realistic neocortical epilepsy models that could provide an explanation of the pathophysiological substrates of neocortical HFOs. In this study, we explored pathological epileptiform network phenomena, particularly HFOs, in a highly realistic murine model of neocortical epilepsy due to focal cortical dysplasia type II (FCDII). FCD was induced in mice by the expression of the human pathogenic mammalian target of rapamycin (mTOR) gene mutation during embryonic stages of brain development. Electrographic recordings from multiple cortical regions in freely moving animals with FCD and epilepsy demonstrated that the FCD lesion generates HFOs from all frequency ranges, ie, gamma, ripples, and fast ripples up to 800 Hz. Gamma ripples were recorded almost exclusively in FCD animals, while fast ripples occurred in controls as well, although at a lower rate. Gamma-ripple activity is particularly valuable for localizing the FCD lesion, surpassing the utility of fast ripples that were also observed in control animals, although at significantly lower rates. Propagating HFOs occurred outside the FCD, and the contralateral cortex also generated HFOs independently of the FCD, pointing to a wider FCD network dysfunction. Optogenetic activation of neurons carrying mTOR mutation and expressing Channelrhodopsin-2 evoked fast ripple oscillations that displayed spectral and morphological profiles analogous to spontaneous oscillations. This study brings experimental evidence that FCDII generates pathological HFOs across all frequency bands and provides information about the spatiotemporal properties of each HFO subtype in FCD. The study shows that mutated neurons represent a functionally interconnected and active component of the FCD network, as they can induce interictal epileptiform phenomena and HFOs.

The molecular genetics of PI3K/PTEN/AKT/mTOR pathway in the malformations of cortical development

Malformations of cortical development (MCD) are a group of developmental disorders characterized by abnormal cortical structures caused by genetic or harmful environmental factors. Many kinds of MCD are caused by genetic variation. MCD is the common cause of intellectual disability and intractable epilepsy. With rapid advances in imaging and sequencing technologies, the diagnostic rate of MCD has been increasing, and many potential genes causing MCD have been successively identified. However, the high genetic heterogeneity of MCD makes it challenging to understand the molecular pathogenesis of MCD and to identify effective targeted drugs. Thus, in this review, we outline important events of cortical development. Then we illustrate the progress of molecular genetic studies about MCD focusing on the PI3K/PTEN/AKT/mTOR pathway. Finally, we briefly discuss the diagnostic methods, disease models, and therapeutic strategies for MCD. The information will facilitate further research on MCD. Understanding the role of the PI3K/PTEN/AKT/mTOR pathway in MCD could lead to a novel strategy for treating MCD-related diseases.

A microglia clonal inflammatory disorder in Alzheimer's Disease

Somatic genetic heterogeneity resulting from post-zygotic DNA mutations is widespread in human tissues and can cause diseases, however few studies have investigated its role in neurodegenerative processes such as Alzheimer's Disease (AD). Here we report the selective enrichment of microglia clones carrying pathogenic variants, that are not present in neuronal, glia/stromal cells, or blood, from patients with AD in comparison to age-matched controls. Notably, microglia-specific AD-associated variants preferentially target the MAPK pathway, including recurrent CBL ring-domain mutations. These variants activate ERK and drive a microglia transcriptional program characterized by a strong neuro-inflammatory response, both in vitro and in patients. Although the natural history of AD-associated microglial clones is difficult to establish in human, microglial expression of a MAPK pathway activating variant was previously shown to cause neurodegeneration in mice, suggesting that AD-associated neuroinflammatory microglial clones may contribute to the neurodegenerative process in patients.

Broadening the scope of multigene panel analysis for adult epilepsy patients

OBJECTIVE

Epilepsy is a suitable target for gene panel sequencing because a considerable portion of epilepsy is now explained by genetic components, especially in syndromic cases. However, previous gene panel studies on epilepsy have mostly focused on pediatric patients.

METHODS

We enrolled adult epilepsy patients meeting any of the following criteria: family history of epilepsy, seizure onset age ≤ 19 years, neuronal migration disorder, and seizure freedom not achieved by dual anti-seizure medications. We sequenced the exonic regions of 211 epilepsy genes in these patients. To confirm the pathogenicity of a novel MTOR truncating variant, we electroporated vectors with different MTOR variants into developing mouse brains.

RESULTS

A total of 92 probands and 4 affected relatives were tested, and the proportion of intellectual disability (ID) and/or developmental disability (DD) was 21.7%. As a result, twelve probands (13.0%) had pathogenic or likely pathogenic variants in the following genes or regions: DEPDC5, 15q12-q13 duplication (n = 2), SLC6A1, SYNGAP1, EEF1A2, LGI1, MTOR, KCNQ2, MEF2C, and TSC1 (n = 1). We confirmed the functional impact of a novel truncating mutation in the MTOR gene (c.7570C > T, p.Gln2524Ter) that disrupted neuronal migration in a mouse model. The diagnostic yield was higher in patients with ID/DD or childhood-onset seizures. We also identified additional candidate variants in 20 patients that could be reassessed by further studies.

SIGNIFICANCE

Our findings underscore the clinical utility of gene panel sequencing in adult epilepsy patients suspected of having genetic etiology, especially those with ID/DD or early-onset seizures. Gene panel sequencing could not only lead to genetic diagnosis in a substantial portion of adult epilepsy patients but also inform more precise therapeutic decisions based on their genetic background.

PLAIN LANGUAGE SUMMARY

This study demonstrated the effectiveness of gene panel sequencing in adults with epilepsy, revealing pathogenic or likely pathogenic variants in 13.0% of patients. Higher diagnostic yields were observed in those with neurodevelopmental disorders or childhood-onset seizures. Additionally, we have shown that expanding genetic studies into adult patients would uncover new types of pathogenic variants for epilepsy, contributing to the advancement of precision medicine for individuals with epilepsy. In conclusion, our results highlight the practical value of employing gene panel sequencing in adult epilepsy patients, particularly when genetic etiology is clinically suspected.

Circumscribing Laser Cuts Attenuate Seizure Propagation in a Mouse Model of Focal Epilepsy

In partial onset epilepsy, seizures arise focally in the brain and often propagate. Patients frequently become refractory to medical management, leaving neurosurgery, which can cause neurologic deficits, as a primary treatment. In the cortex, focal seizures spread through horizontal connections in layers II/III, suggesting that severing these connections can block seizures while preserving function. Focal neocortical epilepsy is induced in mice, sub-surface cuts are created surrounding the seizure focus using tightly-focused femtosecond laser pulses, and electrophysiological recordings are acquired at multiple locations for 3-12 months. Cuts reduced seizure frequency in most animals by 87%, and only 5% of remaining seizures propagated to the distant electrodes, compared to 80% in control animals. These cuts produced a modest decrease in cortical blood flow that recovered and left a ≈20-µm wide scar with minimal collateral damage. When placed over the motor cortex, cuts do not cause notable deficits in a skilled reaching task, suggesting they hold promise as a novel neurosurgical approach for intractable focal cortical epilepsy.

A spectrum of AKT3 activating mutations cause focal malformations of cortical development (FMCDs) in cortical organoids

Focal malformations of cortical development (FMCDs) are brain disorders mainly caused by hyperactive mTOR signaling due to both inactivating and activating mutations of genes in the PI3K-AKT-mTOR pathway. Among them, mosaic and somatic activating mutations of the mTOR pathway activators are more frequently linked to severe form of FMCDs. A human stem cell-based FMCDs model to study these activating mutations is still lacking. Herein, we genetically engineer human embryonic stem cell lines carrying these activating mutations to generate cortical organoids. Mosaic and somatic expression of AKT3 activating mutations in cortical organoids mimicking the disease presentation with overproliferation and the formation of dysmorphic neurons. In parallel comparison of various AKT3 activating mutations reveals that stronger mutation is associated with more severe neuronal migratory and overgrowth defects. Together, we have established a feasible human stem cell-based model for FMCDs that could help to better understand pathogenic mechanism and develop novel therapeutic strategy.

Low-level brain somatic mutations in exonic regions are collectively implicated in autism with germline mutations in autism risk genes

Low-level somatic mutations in the human brain are implicated in various neurological disorders. The contribution of low-level brain somatic mutations to autism spectrum disorder (ASD), however, remains poorly understood. Here, we performed high-depth exome sequencing with an average read depth of 559.3x in 181 cortical, cerebellar, and peripheral tissue samples to identify brain somatic single nucleotide variants (SNVs) in 24 ASD subjects and 31 controls. We detected ~2.4 brain somatic SNVs per exome per single brain region, with a variant allele frequency (VAF) as low as 0.3%. The mutational profiles, including the number, signature, and type, were not significantly different between the ASD patients and controls. Intriguingly, when considering genes with low-level brain somatic SNVs and ASD risk genes with damaging germline SNVs together, the merged set of genes carrying either somatic or germline SNVs in ASD patients was significantly involved in ASD-associated pathophysiology, including dendrite spine morphogenesis (p = 0.025), mental retardation (p = 0.012), and intrauterine growth retardation (p = 0.012). Additionally, the merged gene set showed ASD-associated spatiotemporal expression in the early and mid-fetal cortex, striatum, and thalamus (all p < 0.05). Patients with damaging mutations in the merged gene set had a greater ASD risk than did controls (odds ratio = 3.92, p = 0.025, 95% confidence interval = 1.12-14.79). The findings of this study suggest that brain somatic SNVs and germline SNVs may collectively contribute to ASD-associated pathophysiology.

Pathogenic MTOR somatic variant causing focal cortical dysplasia drives hyperexcitability via overactivation of neuronal GluN2C N-methyl-D-aspartate receptors

OBJECTIVE

Genetic variations in proteins of the mechanistic target of rapamycin (mTOR) pathway cause a spectrum of neurodevelopmental disorders often associated with brain malformations and with intractable epilepsy. The mTORopathies are characterized by hyperactive mTOR pathway and comprise tuberous sclerosis complex (TSC) and focal cortical dysplasia (FCD) type II. How hyperactive mTOR translates into abnormal neuronal activity and hypersynchronous network remains to be better understood. Previously, the role of upregulated GluN2C-containing glutamate-gated N-methyl-D-aspartate receptors (NMDARs) has been demonstrated for germline defects in the TSC genes. Here, we questioned whether this mechanism would expand to other mTORopathies in the different context of a somatic genetic variation of the MTOR protein recurrently found in FCD type II.

METHODS

We used a rat model of FCD created by in utero electroporation of neural progenitors of dorsal telencephalon with expression vectors encoding either the wild-type or the pathogenic MTOR variant (p.S2215F). In this mosaic configuration, patch-clamp whole-cell recordings of the electroporated, spiny stellate neurons and extracellular recordings of the electroporated areas were performed in neocortical slices. Selective inhibitors were used to target mTOR activity and GluN2C-mediated currents.

RESULTS

Neurons expressing the mutant protein displayed an excessive activation of GluN2C NMDAR-mediated spontaneous excitatory postsynaptic currents. GluN2C-dependent increase in spontaneous spiking activity was detected in the area of electroporated neurons in the mutant condition and was restricted to a critical time window between postnatal days P9 and P20.

SIGNIFICANCE

Somatic MTOR pathogenic variant recurrently found in FCD type II resulted in overactivation of GluN2C-mediated neuronal NMDARs in neocortices of rat pups. The related and time-restricted local hyperexcitability was sensitive to subunit GluN2C-specific blockade. Our study suggests that GluN2C-related pathomechanisms might be shared in common by mTOR-related brain disorders.

Balloon cells in malformations of cortical development: friends or foes?

Balloon cells (BCs) are specific pathological marker of cortical malformations during brain development, often associated with epilepsy and development delay. Although a large number of studies have investigated the role of BCs in these diseases, the specific function of BCs as either epileptogenic or antiepileptic remains controversial. Therefore, we reviewed literatures on BCs, delved into the molecular mechanisms and signaling pathways, and updated their profile in several aspects. Firstly, BCs are heterogeneous and some of them show progenitor/stem cell characteristics. Secondly, BCs are relatively silent in electrophysiology but not completely isolated from their surroundings. Notably, abnormal mTOR signaling and aberrant immunogenic process have been observed within BCs-containing malformations of cortical development (MCDs). The question whether BCs function as the evildoer or the defender in BCs-containing MCDs is further discussed. Importantly, this review provides perspectives on future investigations of the potential role of BCs in epilepsy.

Human TSC2 Mutant Cells Exhibit Aberrations in Early Neurodevelopment Accompanied by Changes in the DNA Methylome

Tuberous Sclerosis Complex (TSC) is a debilitating developmental disorder characterized by a variety of clinical manifestations. While benign tumors in the heart, lungs, kidney, and brain are all hallmarks of the disease, the most severe symptoms of TSC are often neurological, including seizures, autism, psychiatric disorders, and intellectual disabilities. TSC is caused by loss of function mutations in the TSC1 or TSC2 genes and consequent dysregulation of signaling via mechanistic Target of Rapamycin Complex 1 (mTORC1). While TSC neurological phenotypes are well-documented, it is not yet known how early in neural development TSC1/2-mutant cells diverge from the typical developmental trajectory. Another outstanding question is the contribution of homozygous-mutant cells to disease phenotypes and whether such phenotypes are also seen in the heterozygous-mutant populations that comprise the vast majority of cells in patients. Using TSC patient-derived isogenic induced pluripotent stem cells (iPSCs) with defined genetic changes, we observed aberrant early neurodevelopment in vitro, including misexpression of key proteins associated with lineage commitment and premature electrical activity. These alterations in differentiation were coincident with hundreds of differentially methylated DNA regions, including loci associated with key genes in neurodevelopment. Collectively, these data suggest that mutation or loss of TSC2 affects gene regulation and expression at earlier timepoints than previously appreciated, with implications for whether and how prenatal treatment should be pursued.

Identification of a mosaic MTOR variant in purified neuronal DNA in a patient with focal cortical dysplasia using a novel depth electrode harvesting technique

OBJECTIVE

Recent studies have identified brain somatic variants as a cause of focal epilepsy. These studies relied on resected tissue from epilepsy surgery, which is not available in most patients. The use of trace tissue adherent to depth electrodes used for stereo electroencephalography (EEG) has been proposed as an alternative but is hampered by the low cell quality and contamination by nonbrain cells. Here, we use our improved depth electrode harvesting technique that purifies neuronal nuclei to achieve molecular diagnosis in a patient with focal cortical dysplasia (FCD).

METHODS

Depth electrode tips were collected, pooled by brain region and seizure onset zone, and nuclei were isolated and sorted using fluorescence-activated nuclei sorting (FANS). Somatic DNA was amplified from neuronal and astrocyte nuclei using primary template amplification followed by exome sequencing of neuronal DNA from the affected pool, unaffected pool, and saliva. The identified variant was validated using droplet digital polymerase chain reaction (PCR).

RESULTS

An 11-year-old male with drug-resistant genetic-structural epilepsy due to left anterior insula FCD had seizures from age 3 years. Stereo EEG confirmed seizure onset in the left anterior insula. The two anterior insula electrodes were combined as the affected pool and three frontal electrodes as the unaffected pool. FANS isolated 140 neuronal nuclei from the affected and 245 neuronal nuclei from the unaffected pool. A novel somatic missense MTOR variant (p.Leu489Met, CADD score 23.7) was identified in the affected neuronal sample. Droplet digital PCR confirmed a mosaic gradient (variant allele frequency = .78% in affected neuronal sample; variant was absent in all other samples).

SIGNIFICANCE

Our findings confirm that harvesting neuronal DNA from depth electrodes followed by molecular analysis to identify brain somatic variants is feasible. Our novel method represents a significant improvement compared to the previous method by focusing the analysis on high-quality cells of the cell type of interest.

Genomic Mosaicism of the Brain: Origin, Impact, and Utility

Genomic mosaicism describes the phenomenon where some but not all cells within a tissue harbor unique genetic mutations. Traditionally, research focused on the impact of genomic mosaicism on clinical phenotype-motivated by its involvement in cancers and overgrowth syndromes. More recently, we increasingly shifted towards the plethora of neutral mosaic variants that can act as recorders of cellular lineage and environmental exposures. Here, we summarize the current state of the field of genomic mosaicism research with a special emphasis on our current understanding of this phenomenon in brain development and homeostasis. Although the field of genomic mosaicism has a rich history, technological advances in the last decade have changed our approaches and greatly improved our knowledge. We will provide current definitions and an overview of contemporary detection approaches for genomic mosaicism. Finally, we will discuss the impact and utility of genomic mosaicism.

Spatial omics reveals molecular changes in focal cortical dysplasia type II

Focal cortical dysplasia (FCD) represents a group of diverse localized cortical lesions that are highly epileptogenic and occur due to abnormal brain development caused by genetic mutations, involving the mammalian target of rapamycin (mTOR). These somatic mutations lead to mosaicism in the affected brain, posing challenges to unravel the direct and indirect functional consequences of these mutations. To comprehensively characterize the impact of mTOR mutations on the brain, we employed here a multimodal approach in a preclinical mouse model of FCD type II (Rheb), focusing on spatial omics techniques to define the proteomic and lipidomic changes. Mass Spectrometry Imaging (MSI) combined with fluorescence imaging and label free proteomics, revealed insight into the brain's lipidome and proteome within the FCD type II affected region in the mouse model. MSI visualized disrupted neuronal migration and differential lipid distribution including a reduction in sulfatides in the FCD type II-affected region, which play a role in brain myelination. MSI-guided laser capture microdissection (LMD) was conducted on FCD type II and control regions, followed by label free proteomics, revealing changes in myelination pathways by oligodendrocytes. Surgical resections of FCD type IIb and postmortem human cortex were analyzed by bulk transcriptomics to unravel the interplay between genetic mutations and molecular changes in FCD type II. Our comparative analysis of protein pathways and enriched Gene Ontology pathways related to myelination in the FCD type II-affected mouse model and human FCD type IIb transcriptomics highlights the animal model's translational value. This dual approach, including mouse model proteomics and human transcriptomics strengthens our understanding of the functional consequences arising from somatic mutations in FCD type II, as well as the identification of pathways that may be used as therapeutic strategies in the future.

NeuroPorator: An open-source, current-limited electroporator for safe in utero gene transfer

BACKGROUND

Electroporation is an effective technique for genetic manipulation of cells, both in vitro and in vivo. In utero electroporation (IUE) is a special case, which represents a fine application of this technique to genetically modify specific tissues of embryos during prenatal development. Commercially available electroporators are expensive and not fully customizable. We have designed and produced an inexpensive, open-design, and customizable electroporator optimized for safe IUE. We introduce NeuroPorator.

METHOD

We used off-the-shelf electrical parts, a single-board microcontroller, and a cheap data logger to build an open-design electroporator. We included a safety circuit to limit the applied electrical current to protect the embryos. We added full documentation, design files, and assembly instructions.

RESULT

NeuroPorator output is on par with commercially available devices. Furthermore, the adjustable current limiter protects both the embryos and the uterus from overcurrent damage. A built-in data acquisition module provides real-time visualization and recordings of the actual voltage/current pulses applied to each embryo. Function of NeuroPorator has been demonstrated by inducing focal cortical dysplasia in mice.

SIGNIFICANCE AND CONCLUSION

The simple and fully open design enables quick and cheap construction of the device and facilitates further customization. The features of NeuroPorator can accelerate the IUE technique implementation in any laboratory and speed up its learning curve.

Mapping recurrent mosaic copy number variation in human neurons

When somatic cells acquire complex karyotypes, they often are removed by the immune system. Mutant somatic cells that evade immune surveillance can lead to cancer. Neurons with complex karyotypes arise during neurotypical brain development, but neurons are almost never the origin of brain cancers. Instead, somatic mutations in neurons can bring about neurodevelopmental disorders, and contribute to the polygenic landscape of neuropsychiatric and neurodegenerative disease. A subset of human neurons harbors idiosyncratic copy number variants (CNVs, "CNV neurons"), but previous analyses of CNV neurons are limited by relatively small sample sizes. Here, we develop an allele-based validation approach, SCOVAL, to corroborate or reject read-depth based CNV calls in single human neurons. We apply this approach to 2,125 frontal cortical neurons from a neurotypical human brain. SCOVAL identifies 226 CNV neurons, which include a subclass of 65 CNV neurons with highly aberrant karyotypes containing whole or substantial losses on multiple chromosomes. Moreover, we find that CNV location appears to be nonrandom. Recurrent regions of neuronal genome rearrangement contain fewer, but longer, genes.