Genetic autophagy enhancement improves neuroinflammation and recovery after spinal cord injury via transcriptomic modulation

Background Autophagy, a conserved cellular process responsible for degrading and recycling damaged organelles and proteins, plays a critical role in maintaining cellular homeostasis, particularly under stress conditions such as neurotrauma. In experimental models of spinal cord injury (SCI), dysregulated autophagy is closely linked to secondary injury cascades, particularly post-injury inflammatory responses. These inflammatory processes are exacerbated by genetic inhibition of autophagy and alleviated by pharmacological enhancement. Furthermore, SCI triggers neuropathological changes in the brain, often accompanied by cognitive impairments. However, the molecular mechanisms underlying these effects remain largely unclear. Methods Three-month-old male Becn1 ^F121A/F121A knock-in (BMut) mice, which exhibit enhanced autophagy, and wild-type (WT) mice were subjected to moderate thoracic spinal cord contusion. At 3 days post-injury, spinal cord (SPC) tissues were collected and processed using the NanoString Neuroinflammation Panel. In the chronic cohort (10 weeks post-injury), locomotor recovery was monitored using the Basso Mouse Scale (BMS) scoring. At endpoint, cognitive function was assessed via behavioral tests. Tissues from the SPC, hippocampus, and somatosensory cortex were collected for bulk RNA sequencing. Lesion volume and spared white matter (SWM) in the spinal cord were assessed, along with Iba-1 ⁺ microglial morphology analysis and doublecortin-positive immature neurons in the hippocampal dentate gyrus (DG). Results Transcriptomic analysis of BMut mouse SPC at 3 days post-injury revealed enhanced autophagy flux, reduced inflammatory responses, and altered microglial function and immune activity. Ten weeks after injury, BMut mice exhibited distinct transcriptomic profiles in the SPC, somatosensory cortex, and hippocampus. Further analyses revealed that the Becn1 ^F121A/F121A mutation enhanced autophagy and altered inflammatory responses to SCI across all three regions. Behavioral assessments demonstrated improved functional recovery in BMut mice, accompanied by better-preserved SWM and reduced lesion volume. Immunofluorescence staining analysis showed that the Becn1 ^F121A/F121A mutation reduced microglial activation and enhanced neurogenesis in the hippocampal DG region. Conclusions Our study showed that genetic enhancement of autophagy altered transcriptomic responses—particularly inflammation—after SCI, reducing neuropathology in the spinal cord and brain and improving function. This is the first evidence linking autophagy enhancement to modulation of neuroinflammation after SCI, highlighting its therapeutic potential.