Single-Nuclei RNA-Sequencing Resolves Cell-Type Specific Transcriptional Changes in Pediatric Epilepsy
Abstract number :
1.146
Submission category :
2. Translational Research / 2A. Human Studies
Year :
2025
Submission ID :
841
Source :
www.aesnet.org
Presentation date :
12/6/2025 12:00:00 AM
Published date :
Authors :
Presenting Author: Ashton Holub, PhD – Nationwide Children's Hospital
Adithe Rivaldi, BS – Nationwide Children's Hospital
Jesse Westfall, BS – Nationwide Children's Hospital
Jaye Navarro, BS – Nationwide Children's Hospital
Allison Daley, MS – Nationwide Children's Hospital
Jonathan Pindrik, MD – Division of Pediatric Neurosurgery, Department of Neurological Surgery, Nationwide Children’s Hospital and The Ohio State University College of Medicine, Columbus, OH
Ammar Shaikhouni, MD, PhD – Nationwide Children’s Hospital and The Ohio State University College of Medicine, Columbus, OH
Daniel Boue, MD, PhD – Nationwide Children's Hospital
Diana Thomas, MD, PhD – Nationwide Children's Hospital
Christopher Pierson, MD – Nationwide Children's Hospital
Elaine Mardis, PhD – Nationwide Children's Hospital
Adam Ostendorf, MD – Division of Neurology, Department of Pediatrics, Nationwide Children’s Hospital and The Ohio State University College of Medicine, Columbus, OH
Daniel Koboldt, MS – Nationwide Children's Hospital
Katherine Miller, PhD – Nationwide Children's Hospital
Tracy Bedrosian, PhD – Nationwide Children's Hospital
Rationale: Approximately 1 in 150 children are diagnosed with epilepsy, with one-third presenting with intractable, drug-resistant seizures. For these patients, surgical resection of affected brain tissue is an important treatment option, though 50% experience seizure recurrence. Focal cortical dysplasia (FCD), characterized by disrupted cortical layering and ectopic neurons, is a major contributor to pediatric epilepsy, yet its molecular underpinnings remain poorly understood. Single-nuclei RNA sequencing (snRNA-seq) enables cell-type-specific resolution of gene expression changes, overcoming the limitations of bulk RNA-seq. We hypothesize that epilepsy involves distinct transcriptional alterations across specific cell types. Here, we present snRNA-seq analysis of resected brain tissue from 14 pediatric patients with FCD to identify differentially expressed genes (DEGs) and elucidate cell-type-specific molecular signatures of epilepsy.
Methods: Patient tissues were obtained through our Somatic Epilepsy translational research protocol at Nationwide Children’s Hospital; post-mortem controls were sourced from the NIH NeuroBioBank. Nuclei were isolated from frozen tissue and sequenced using the 10x Genomics 3’-single cell gene expression assay. Data were processed using the Seurat package in R. Cells were filtered for nCount_RNA < 100,000 and > 1,000, nFeature_RNA > 500, and mitochondrial content < 2%. Cell types were annotated using the Allen Brain Cell Atlas – Whole Human Brain reference via the FindTransferAnchors function. DEGs were identified using pseudobulk DESeq2 analysis (by tissue sample) between matched patient and control cell types, with an adjusted p-value threshold of ≤ 0.1.
Translational Research