Integrated Multi-Omics Profiling Identifies CD84-Associated Microglial Alterations in Focal Cortical Dysplasia Type II

Yubao Fang,* Shengyu Yang,* Lei Lei,* Yinchao Li, Yaqian Zhang, Tiancai Huang, Liemin Zhou Department of Neurology, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, People’s Republic of China*These authors contributed equally to this workCorrespondence: Liemin Zhou, Email [email protected]: Focal cortical dysplasia type II (FCDII) is a major cause of drug-resistant epilepsy in children, yet its molecular pathogenesis remains poorly characterized. Accumulating evidence has underscored the critical role of persistent neuroinflammatory activity in the pathogenesis of focal cortical dysplasia.Methods: We employed an integrated multi-omics approach to dissect the molecular pathology of FCDII. This included data-independent acquisition mass spectrometry (DIA-MS) proteomics and re-analysis of public transcriptomic datasets. Differential expression analysis, protein-protein interaction (PPI) network construction, and hub gene identification were performed. Key findings were validated using quantitative real-time PCR (qPCR) and further investigated through analysis of single-cell RNA sequencing (scRNA-seq) data to resolve cellular heterogeneity and cell-cell communication.Results: Proteomic profiling of FCDII tissue identified 460 differentially expressed proteins (DEPs) enriched in cortical development, cytoskeletal organization, and immune–inflammatory signaling. Protein–protein interaction (PPI) network analysis further prioritized several hub molecules, among which the pro-inflammatory glycoprotein CD84 exhibited consistent upregulation across both proteomic and transcriptomic datasets. Single-cell analysis revealed that CD84 expression was preferentially localized to a microglial subpopulation characterized exhibiting elevated inflammation-related signatures, with particularly prominent enrichment in FCDIIB samples. CD84-positive microglia also demonstrated increased predicted interactions with astrocytes, neurons, and endothelial cells through signaling pathways involving colony-stimulating factor (CSF), CX3C motif chemokine, macrophage migration inhibitory factor (MIF), and somatostatin-related signaling.Conclusion: Our multi-omics approaches suggest a potential role for CD84 in influencing microglial inflammatory states and in shaping their predicted interactions with astrocytes, neurons, and endothelial cells in FCDII. These findings offer preliminary molecular clues that may inform future mechanistic investigations of microglial alterations in this disorder.Keywords: focal cortical dysplasia type II, multi-omics integration, neuroinflammation, CD84, microglial activation