Integrating single-cell RNA sequencing and spatial multi-omics reveals the molecular signature of regeneration after spinal cord injury

BACKGROUND: A certain degree of self-repair is initiated following spinal cord injury (SCI). Although intraneuronal regeneration and a supportive growth environment are limited, they serve as the foundation for functional recovery after SCI. METHODS: In this study, we conducted single-cell RNA sequencing combined with spatial transcriptomics and spatial metabolomics to reveal the spatial molecular characteristics of self-repair processes after SCI at single-cell resolution. RESULTS: We identified three cell subsets-Mic2 (a microglia subset), Mac4 (a macrophage subset), and Fib4 (a fibroblast subset)-that express markers associated with spinal cord repair. Mic2 and Mac4 exhibit clustered spatial distribution patterns, whereas Fib4 is predominantly located around the injured spinal cord. Additionally, Mic2 is predominantly distributed in the white matter, particularly in the dorsal region of the injured spinal cord, and exhibits high expression of taurine. Mac4 and Fib4 exhibit high expression of copalic acid and uridine, respectively. CONCLUSIONS: In this study, we have identified three distinct cell subsets that express markers associated with wound healing and may promote regenerative processes, and we have determined their spatial transcriptional and metabolic features enriched within these regions. Our dataset represents a valuable resource that offers novel mechanistic insights into the pathobiology of spinal cord injury.