Bergenin attenuates traumatic brain injury via inhibition of microglial PFKFB3-driven glycolytic–inflammatory crosstalk

Traumatic brain injury (TBI) initiates a complex cascade of neuroinflammatory and metabolic disturbances that exacerbate neuronal loss and neurological dysfunction. Microglial glycolytic reprogramming, particularly driven by the rate-limiting enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3), has emerged as a key driver of secondary injury. Bergenin, a naturally occurring C-glycoside with antioxidant and anti-inflammatory activities, has demonstrated multi-organ protective potential, but its underlying mechanisms of immunometabolic regulation in TBI remain unclear. Here, we integrated transcriptomic profiling, weighted gene co-expression network analysis (WGCNA), and multi-database target prediction to identify PFKFB3 as a critical target of Bergenin in TBI. Machine-learning-based screening and molecular docking, dynamics, and surface plasmon resonance (SPR) assays confirmed a direct and stable Bergenin–PFKFB3 interaction (KD = 6.33 μM). In vivo, Bergenin improved neurological recovery in TBI mice, evidenced by reduced neuronal damage, apoptosis, and pro-inflammatory cytokine production (TNF-α, IL-6, and IL-1β). It also downregulated PFKFB3 and its downstream glycolytic enzymes (HK2, PKM2, and LDHA), indicating attenuation of glycolytic activation after injury. Single-cell transcriptomic analysis revealed microglia-enriched PFKFB3 expression associated with inflammatory signaling and altered intercellular communication patterns. In vitro, Bergenin treatment and silencing of PFKFB3 inhibited LPS + IFN-γ–induced microglial activation, reduced glycolytic activity and promoted a phenotypic shift from pro-inflammatory to anti-inflammatory states, with no further enhancement upon their combination. These findings identify PFKFB3 as an immunometabolic regulation hub in TBI and uncover Bergenin as a promising natural compound that directly targets microglial PFKFB3, reprograms immunometabolic pathways, and alleviates post-traumatic neuroinflammation. Bergenin attenuates traumatic brain injury–induced neuroinflammation by inhibiting microglial PFKFB3-driven glycolytic reprogramming, thereby disrupting the glycolytic–inflammatory crosstalk and promoting an anti-inflammatory microglial phenotype. • Traumatic brain injury features strong metabolic–inflammatory dysregulation requiring new therapeutic targets. • Multi-omics and machine-learning analyses identify PFKFB3 as a Bergenin-associated immunometabolic hub. • Bergenin inhibits PFKFB3-linked glycolytic and inflammatory activation and improves post-traumatic outcomes in mice. • Single-cell sequencing localizes PFKFB3 upregulation predominantly to microglia in TBI lesions. • Bergenin suppresses LPS + IFN-γ–induced PFKFB3-associated microglial activation and glycolysis in vitro.