Integrative Transcriptomic Mapping Reveals C1Q/AP-Like Microglial State Reconfiguration in Temporal Lobe Epilepsy with Hippocampal Sclerosis

Drug-resistant epilepsy involves persistent remodeling of the epileptogenic tissue microenvironment. In temporal lobe epilepsy with hippocampal sclerosis (TLE-HS), it remains unclear whether microglia exhibit uniform inflammatory activation or structured state-level reconfiguration. We integrated single-cell RNA sequencing data from GSE190452 with an independent bulk RNA sequencing cohort, GSE256068. Microglial state signatures derived from the single-cell dataset were projected into bulk tissue, and abundance-adjusted models and a non-overlap sensitivity analysis were used to distinguish state-associated remodeling from changes in microglial representation. Associations of ST6GAL1 and CX3CR1 with microglial state programs were explored. HMC3 human microglia-like cells were used for exploratory CX3CL1–CX3CR1 pathway-level assays under magnesium-free conditioned-medium stimulation. Single-cell analysis identified 5,963 microglia/myeloid cells and nine transcriptional state programs, with marked inter-individual heterogeneity and no consistent global inflammatory shift. In the bulk validation cohort, a C1Q/antigen-presentation-like program was the most reproducibly elevated microglial signature in TLE-HS and remained associated with disease status after adjustment for microglial abundance. Inflammatory-output signals were attenuated after abundance adjustment, whereas amplification-prone signatures showed limited reproducibility. ST6GAL1 and CX3CR1 preferentially tracked the C1Q/antigen-presentation-like program. In HMC3 cells, CX3CL1 treatment was accompanied by lower inflammatory mediator release and reduced nuclear factor-κB p65 nuclear localization, while CX3CR1 antagonism partially reversed these patterns. Human epileptogenic tissue exhibits structured microglial state reconfiguration rather than uniform immune activation. The C1Q/antigen-presentation-like program represents a reproducible lesion-associated signature, while ST6GAL1/CX3CR1 findings remain exploratory candidate associations.