Accurate determination of the timing and progression of traumatic brain injury (TBI) is critical in forensic pathology, particularly for reconstructing injury events and estimating post-traumatic intervals. However, conventional timing approaches of TBI rely on limited pathological features and often lack sufficient accuracy. To address this limitation, we re-analyzed publicly available single-cell RNA-seq datasets from GEO (GSE269748 and GSE160763) and integrated murine cortical transcriptomes across three post-injury stages—acute (24 h), subacute (7 days), and chronic (6 months)—to characterize time-resolved neuronal molecular changes after TBI. Neuron-focused differential expression and functional enrichment analyses revealed a progression from early stress and inflammatory-response programs toward later synaptic and neurodegeneration-associated alterations. We further curated representative gene sets for 14 regulated cell-death programs and quantified their activity using AUCell-derived AUC scoring, identifying stage-dependent shifts in death-associated transcriptional signatures, with higher necroptosis- and pyroptosis-associated signals in the acute phase and increased ferroptosis- and autophagic cell death–associated signals in the chronic phase, accompanied by transcriptional patterns consistent with altered iron handling and glutathione metabolism. This re-analysis provides a time-resolved, neuron-centered molecular framework that may support forensic estimation of injury timing and offers insight into mechanisms of secondary brain injury.
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