Integrative analysis of single-cell epigenomes and transcriptomes to reveal novel biomarkers in Epilepsy

Abstract

Focal Cortical Dysplasias (FCDs) are a type of malformation of the cerebral cortex that appears mainly in childhood, and whose treatment requires surgical intervention to control severe epileptic seizures. Despite significant advances in the molecular and neuroimaging pathological characterization of FCDs lesions, there is still a large gap regarding the role of abnormal cells present in the FCD lesions in children. In addition, the paucity of molecular data on the human brain during childhood hinders research into the causes of childhood Epilepsy, as it makes it difficult to reliably determine the molecular and cellular processes disturbed by these conditions. Recent single-cell sequencing technologies are able to obtain genetic information at the level of individual cells, thereby allowing the discovery of the cellular diversity of complex tissues. Notably, the human brain is composed of several cell types including astrocytes, oligodendrocytes, as well as several types of excitatory and inhibitory neurons that make up the different cortical layers. Thus, single-cell sequencing provides an accurate view of the cellular composition of complex organs such as the human brain, thus helping to uncover cell types involved in neurological diseases.In this context, this project will use recent single-cell sequencing technologies to create a cell atlas in order to catalog the cellular diversity of the human infant brain associated with the development of Epilepsy. Tissue samples collected from donors aged between 3 to 15 years diagnosed with FCD Type IIb, from which both lesions and normal tissues are available will be sequenced. Samples will be profiled using the 10X Genomics platform and the Multiome kit that allows simultaneous measurement of the epigenome (scATAC-seq) and transcriptome (snRNA-seq) from single cells. The resulting data will be analyzed with bioinformatics tools in order to discover cell types and neuronal regulatory networks linked to infant brain development and disease. In addition, we will characterize the different cell types present in Type IIb FCD lesions, and thus determine cell populations that may be involved in the disease. The integration of open chromatin and gene expression will enable the identification of distal regulatory regions (enhancers) that control gene expression in diverse types of brain cells, allowing us to understand the epigenetic control of genes associated with the disease. Furthermore, we will compare epigenetic and transcriptomic changes between the adult and infant brain under normal conditions, considering that the adult brain was recently mapped with single-cell sequencing.Overall, the cell atlas is expected to reveal the cellular diversity of neuronal and non-neuronal populations associated with the development of childhood Epilepsy. The data generated in this project will serve as a reference for the study of childhood neurological diseases and will be made available to the scientific community through the Human Cell Atlas. (AU)