Background: Neuropathic pain (NP) following spinal cord injury (SCI) remains a major clinical challenge with limited therapeutic options. This study investigated the mechanism by which repetitive transcranial magnetic stimulation (rTMS) alleviates SCI-induced neuropathic pain (SCI-NP) via the GATA-binding protein 3 (GATA3)-Perforin 1 (PRF1) signaling axis.

Methods: Public transcriptomic datasets (GSE126611, GSE226238, GSE230149) were analyzed to identify candidate rTMS-responsive targets using protein-protein interaction (PPI) and functional enrichment analyses. In vivo, a contusive SCI model was induced in male Sprague–Dawley (SD) rats, followed by rTMS treatment (15 Hz, 6 weeks). Pain behaviors were assessed by Hargreaves and von Frey tests. Cytokine expression was quantified by enzyme-linked immunosorbent assay (ELISA), and GATA3/PRF1 expression was measured by Quantitative real-time polymerase chain reaction (qPCR) and Western blot. In vitro, binding of GATA3 to the PRF1 promoter was validated in rat spinal neurons using luciferase reporter assays and chromatin immunoprecipitation (ChIP). Functional rescue experiments were performed by intrathecal overexpression of GATA3.

Results: Bioinformatic analyses identified a regulatory interaction between GATA3 and PRF1. rTMS treatment significantly reduced mechanical allodynia and thermal hyperalgesia (p < 0.05), downregulated pro-inflammatory cytokines (interleukin (IL)-1β, IL-6, tumor necrosis factor-α (TNF-α); p < 0.001), upregulated IL-10 (p < 0.001), and suppressed expression of GATA3 and PRF1 (p < 0.001). Mechanistically, GATA3 directly bound the PRF1 promoter. GATA3 overexpression abolished rTMS-mediated analgesic and anti-inflammatory effects (p < 0.05).

Conclusion: These findings suggest that rTMS alleviates SCI-NP by inhibiting GATA3-mediated transcriptional activation of PRF1, thereby reducing neuroinflammation.