A multi-omics atlas reveals spatially resolved sphingolipid metabolic reprogramming after spinal cord injury

Secondary injury cascades following spinal cord injury (SCI) are closely associated with local metabolic dysregulation and persistent neuroinflammation. However, the spatiotemporal patterns of alterations centered on sphingolipid metabolism within the injury microenvironment, as well as their specific regulatory mechanisms in relation to neuroimmune inflammation, remain poorly understood at a systematic level. In this study, we integrated high-throughput lipidomics, spatial transcriptomics, and single-cell RNA sequencing (scRNA-seq) of multiple SCI models, to systematically construct a multidimensional spatiotemporal atlas of sphingolipid metabolism following injury. Lipidomics analysis revealed remodeling of sphingolipid metabolism, characterized by the progressive accumulation of neurotoxic sphingolipid metabolites and the depletion of myelin-associated lipids. Spatial transcriptomics demonstrated that regions of sphingolipid metabolism were strikingly confined to the ‘inflammatory infiltration core’ and the ‘scar interface’. At the single-cell level, microglia were identified as the central cellular mediators of this metabolic reprogramming. Notably, we discovered a distinct microglial subpopulation characterized by high expression of the peroxisomal enzyme Hsd17b4 and the disease-associated marker Spp1, termed the ‘high-sphingolipid metabolism’ subtype. Pseudotime trajectory analysis indicated that sustained elevation of sphingolipid metabolic activity constitutes a potential determinant that prevents microglia from returning to homeostasis and drives their maladaptive polarization toward a chronic pathological phenotype. Immunofluorescence staining confirmed the specific enrichment of Hsd17b4 + /Spp1 + microglia within the injury core. Our findings demonstrate that sphingolipid metabolism reprogramming in microglia represents a key mechanistic step in the propagation of secondary injury following SCI. These results provide novel theoretical foundations and potential therapeutic targets for modulating the immuno-metabolic microenvironment to promote functional recovery after spinal cord injury.