Hippocampal tandem mass tag (TMT) proteomics analysis during kindling epileptogenesis in rat

• Epileptogenesis-associated hippocampus proteins alterations were investigated using electrical kindling model. • Deferentially expressed signaling protein profiles showed stage-specific changes during epileptogenesis. • Gene ontology analysis on differentially expressed proteins (DEPs) showed significant changes of proteins involved in immune responses during S3/C0, regulation of synaptic plasticity like during S5/S3, and nervous system development throughout S5/C0.There were also proteins which were altered commonly among all three phases. • The pathway enrichment analysis of DEPs discovers molecular connections between phases and we have found that the targets were analyzed throughout all three phases were highly involved in the PPI network analysis as hub nodes. Epilepsy is a neurological disorder that remains difficult to treat due to the lack of a clear molecular mechanism and incomplete understanding of involved proteins. To identify potential therapeutic targets, it is important to gain insight into changes in protein expression patterns related to epileptogenesis. One promising approach is to analyze proteomic data, which can provide valuable information about these changes. In this study, to evaluate the changes in gene expression during epileptogenesis, LC-MC 2 analysis was carried out on hippocampus during stages of electrical kindling in rat models. Subsequently, progressive changes in the expression of proteins were detected as a result of epileptogenesis development. In line with behavioral kindled seizure stages and according to the proteomics data, we described epileptogenesis phases by comparing Stage3 versus Control (S3/C0), Stage5 versus Stage3 (S5/S3), and Stage5 versus Control group (S5/C0). Gene ontology analysis on differentially expressed proteins (DEPs) showed significant changes of proteins involved in immune responses like Csf1R, Aif1 and Stat1 during S3/C0, regulation of synaptic plasticity like Bdnf, Rac1, CaMK, Cdc42 and P38 during S5/S3, and nervous system development throughout S5/C0 like Bdnd, Kcc2 and Slc1a3.There were also proteins like Cox2, which were altered commonly among all three phases. The pathway enrichment analysis of DEPs was also done to discover molecular connections between phases and we have found that the targets like Csf1R, Bdnf and Cox2 were analyzed throughout all three phases were highly involved in the PPI network analysis as hub nodes. Additionally, these same targets underwent changes which were confirmed through Western blotting. Our results have identified proteomic patterns that could shed light on the molecular mechanisms underlying epileptogenesis which may allow for novel targeted therapeutic strategies.