Multi-Omic Analysis of Glutamate Excitotoxicity in Primary Neuronal Cultures

Glutamate excitotoxicity plays a critical role in neurodegeneration by triggering NMDA receptor hyperactivation, leading to elevated synaptic calcium levels and subsequent neuronal death. To better understand how glutamate affects neurons in neurological diseases, we conducted a comprehensive analysis of molecular changes at the transcriptome and kinome levels. We used primary cortical cultures from rat embryos to study glutamate-induced excitotoxicity. Intermediate doses of glutamate (250 μM) produced significant neurotoxic effects, whereas high and low doses resulted in less cell mortality, aligning with previous findings related to calcium influx. Transcriptional analysis identified BTG2, NPAS4, and CCN1 as the most significantly differentially expressed genes following 250 μM glutamate treatment in neurons. Dkk2, a Wnt antagonist, exhibited the highest log fold change among the significantly differentially expressed genes. Gene set enrichment analysis identified 1127 significant pathways. Perturbagen analysis revealed 2811 unique concordant signatures and 1071 unique discordant signatures. Kinome array profiling indicated activation of PKA and PKG kinases, which regulate signaling pathways essential for synaptic plasticity-related gene expression. Multi-omic integration of transcriptome and kinome data revealed enrichment of response to oxidative stress, actin filament organization, and regulation of apoptotic processes pathways. The Wnt signaling pathway emerged as a pivotal factor in the early stages of axon differentiation and growth, as well as in shaping axonal behavior and dendrite development. Moreover, the interplay between MAPK and Wnt signaling pathways likely impacts cellular differentiation processes. Our findings highlight a prominent role for p38/MAPK and stress-activated MAPK pathways, with specific activation of the MAPK/ERK signaling pathway in response to excitotoxic neuronal damage in vitro. In conclusion, glutamate excitotoxicity induces molecular changes at the transcriptome and kinome levels that include elements of the MAPK and WNT biological pathways.