Unraveling Epilepsy Biomarkers through Single-Cell Sequencing and GEO Data Integration: A Focus on Parthanatos Pathway

Background: Epilepsy is a chronic brain disorder with complex molecular mechanisms. Parthanatos, a PARP-1-dependent programmed cell death pathway, has been implicated in neurodegenerative diseases and mitochondrial dysfunction, which are closely associated with epilepsy pathogenesis. However, the role of parthanatos-related genes (PRGs) in epilepsy remains unclear. This study aimed to explore PRGs as potential biomarkers for epilepsy and elucidate their molecular mechanisms. Methods: Transcriptome data from patients with unclassified epilepsy and healthy controls were obtained from the Gene Expression Omnibus (GEO) and Biostudies databases (GSE143272 and E-MTAB-3123). Differential gene expression analysis, weighted gene co-expression network analysis (WGCNA), and functional enrichment were performed. Machine learning models (Random Forest, GLM, SVM) were employed to identify biomarkers. Immune infiltration, regulatory networks, and single-cell RNA sequencing (scRNA-seq) analyses were conducted to investigate cellular and molecular interactions. Key findings were validated using RT-qPCR. Results: Five biomarkers—FAM91A1, TSPAN2, HNRNPH2, HAUS4, and SRPK1—were identified, with AUC values >0.7 in both datasets. These biomarkers showed significant positive correlations with activated dendritic cells and negative correlations with activated CD8 T cells. These biomarkers were commonly enriched in the RIBOSOME pathway. Single-cell analysis revealed significant differential expression of FAM91A1, TSPAN2, and HNRNPH2 in oligodendrocyte progenitor cells (OPCs). RT-qPCR validation confirmed upregulation of SRPK1, FAM91A1, and TSPAN2 in epilepsy patients, supporting their diagnostic potential. Conclusion: This study identified five PRG-related biomarkers for epilepsy, highlighting their roles in immune modulation and OPC dysfunction. The findings provide novel insights into epilepsy pathogenesis and offer potential targets for clinical diagnosis and therapeutic intervention.