Project description:Focal Cortical Dysplasia (FCD) is a major cause of drug-resistant focal epilepsy in children and the clinico-pathological classification remains a challenging issue in daily practice. With the recent progress in DNA methylation based classification of human brain tumors we examined, whether genomic DNA methylation and gene expression analysis can be used to also distinguish human FCD subtype
Project description:We generated cortical organoids from four FCD patients. To generate cortical organoids, we used induced pluriplotent stem cells (iPSCs) obtained from skin biopsy from these FCD selected patients and healthy controls. We extrated RNA samples from the cortical organoids to do customized panel of gene expression. Gene expression using NanoString Human Neuropathology Panel from four FCD patients and four controls
Project description:Focal Cortical Dysplasia (FCD) is a major cause of drug-resistant focal epilepsy in children and the clinico-pathological classification remains a challenging issue in daily practice. With the recent progress in DNA methylation based classification of human brain tumors we examined, whether genomic DNA methylation and gene expression analysis can be used to also distinguish human FCD subtype
Project description:Sequencing of the mTOR/GATOR pathway panel to search for mosaic mutations in brain tissue removed from surgery for the treatment of epilepsy, and in peripheral blood from patients with FCD.
Project description:In females with X-linked genetic disorders, wild-type and mutant cells coexist within brain tissue because of random X-chromosome inactivation. This cellular mosaicism leads to phenotypic variability and poses significant challenges for interpreting the effects of X-linked mutant alleles on gene expression. We present a single-nucleus RNA sequencing approach that resolves mosaicism by using single nucleotide polymorphisms in genes that are expressed in cis with the X-linked mutation to determine whether individual nuclei express the wild-type or mutant allele even when the mutant gene is not directly detected. This approach enables genome-wide comparisons of gene expression between mutant and wild-type cells within the same individual and eliminates the variability introduced by comparisons to controls with different genetic backgrounds. We apply this approach to mosaic female mouse models and humans with Rett syndrome, an X-linked neurodevelopmental disorder caused by mutations in the methyl-DNA-binding protein MECP2, and reveal that cell-type-specific DNA methylation patterns largely predict the degree of gene upregulation by MECP2 in specific neuronal subtypes. The approach described here can be broadly applied to the characterization of gene expression in additional mosaic X-linked conditions.
Project description:Focal cortical dysplasia (FCD) is a heterogeneous group of cortical developmental malformations that constitute a common cause of medically intractable epilepsy. Multiomic integration was conducted via single-nucleus RNA sequencing (snRNA-seq) and single-nucleus assays for transposase-accessible chromatin sequencing (snATAC-seq) to analyse cell type-specific alterations in chromatin accessibility and correlate them with gene expression changes in the epileptogenic cortex of FCD type IIIa (FCD IIIa).
