Mosaic FCD
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB47932 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
2019-05-13 | GSE128300 | GEO
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
2022-01-01 | GSE174605 | GEO
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
2019-05-13 | GSE128299 | GEO
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.
2021-10-17 | PRJEB48128 | EVA
Project description:Transcriptomes distinguish human FCD subtypes
| PRJNA527060 | ENA
Project description:Genomic DNA methylation distinguishes human FCD subtypes
| PRJNA527061 | ENA
Project description:Modeling Focal Cortical Dysplasia (FCD) using cortical organoids
| PRJNA730718 | ENA
Project description:Transcriptome and Genomic DNA methylation distinguishes human FCD subtypes
| PRJNA527057 | ENA
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.
2018-11-15 | GSE113903 | GEO
Project description:Focal Cortical Dysplasia (FCD) is a frequent cause of drug-resistant focal epilepsy in children and young adults. The international FCD classifications of 2011 and 2022 have identified several clinico-pathological subtypes, either occurring isolated, i.e., FCD ILAE Type 1 or 2, or in association with a principal cortical lesion, i.e., FCD Type 3. Here, we addressed the DNA methylation signature of a previously described new subtype of FCD 3D occurring in the occipital lobe of very young children and microscopically defined by neuronal cell loss in cortical layer 4. We studied the DNA methylation profile using 850K BeadChip arrays in a retrospective cohort of 104 patients with FCD 1A, 2A, 2B, 3D, TLE without FCD, and 16 postmortem specimens without neurological disorders as controls, operated in China or in Germany. DNA was extracted from formalin-fixed paraffin-embedded tissue blocks with microscopically confirmed lesions, and DNA methylation profiles were bioinformatically analyzed with a recently developed deep learning algorithm. Our results revealed a distinct position of FCD 3D in the DNA methylation map of common FCD subtypes, also different from non-FCD epilepsy surgery controls or non-epileptic postmortem controls. Within the FCD 3D cohort, the DNA methylation signature separated three histopathology subtypes, i.e., fibrotic scarring around porencephalic cysts, loss of layer 4, and Rasmussen encephalitis. Differential methylation in FCD 3D with loss of layer 4 specifically mapped to biological pathways related to neurodegeneration, biogenesis of ECM components, axon guidance, and regulation of the actin cytoskeleton. Our data suggest that DNA methylation signatures in cortical malformations are not only of diagnostic value but also phenotypically relevant, providing the molecular underpinnings of structural and histopathological features associated with epilepsy. Further studies will be necessary to confirm these results and clarify their functional relevance and epileptogenic potential in these difficult-to-treat children.
2023-08-21 | GSE227239 | GEO