Multi-omics mapping identifies a C/EBPβ-S100a4⁺ macrophage axis as a therapeutic target in acute spinal cord injury

Acute neuroinflammation drives secondary degeneration after spinal cord injury (SCI), yet the precise immune cell states and upstream regulatory circuits that initiate this response remain unresolved. Defining these early-state determinants at multi-omics resolution is essential for identifying mechanistically grounded therapeutic targets. We implemented an integrated multi-omics framework combining high-temporal-resolution single-cell RNA sequencing, bulk transcriptomics, histological validation, and systems-level network modeling across uninjured and early post-injury time points. Cell-cell communication analysis delineated intercellular signaling architecture within the acute lesion niche. Transcriptional regulatory network inference with in silico perturbation identified candidate master regulators. Network-based compound prioritization and target engagement validation were followed by functional testing in activated macrophages and a mouse SCI model. We resolved a temporally restricted S100a4 + macrophage state that rapidly emerged after injury, peaked at 1 day, and subsequently contracted. This state was defined by a coordinated transcriptional program integrating enhanced migratory capacity, amplified pro-inflammatory and pyroptotic signaling, and repression of homeostatic and reparative modules, constituting the dominant acute inflammatory signature at the tissue level. Systems-level analysis established a Cebpb -centered regulatory circuitry governing this state, thereby defining a C/EBPβ-S100a4 + macrophage axis as a principal driver of early neuroinflammation. Network topology positioned this axis as a densely connected and self-reinforcing hub within the injury microenvironment. Computational drug prioritization identified baicalein as a candidate regulator of C/EBPβ-dependent signaling. ChIP-qPCR and nuclear-cytoplasmic fractionation validated that baicalein effectively reduced the nuclear translocation of C/EBPβ and its binding to the S100a4 promoter. Experimental validation demonstrated that baicalein suppressed C/EBPβ expression, attenuated downstream inflammatory and pyroptotic pathways, and significantly improved functional recovery following SCI. This study delineates a C/EBPβ-S100a4 + macrophage axis that mechanistically structures the acute inflammatory landscape of SCI and represents a tractable therapeutic vulnerability. These findings advance a state-specific, network-informed framework for early immunomodulation in spinal cord injury.