Identification of stress granule-related potential biomarkers in spinal cord injury: an integrated analysis using bulk RNA and single-cell RNA sequencing

Spinal cord injury (SCI) is a debilitating condition with complex molecular mechanisms. Stress granules (SGs) have been implicated in cellular stress responses, but their role in SCI remains unclear. This study aimed to identify SG-related potential biomarkers and elucidate their functional mechanisms in SCI. Transcriptomics data, single-cell RNA sequencing (scRNA-seq) data, and SG-related genes (SG-RGs) were obtained from public databases. Candidate genes were identified by intersecting differentially expressed genes (DEGs) with SG-RGs. The candidate genes were subjected to functional enrichment analysis. Potential biomarkers were further obtained by protein–protein interaction (PPI), and expression level validation. The murine biomarkers were mapped to human homologous biomarkers. The subcellular localization, tissue expression, and drug predictions of potential biomarkers were explored. Subsequently, scRNA-seq analysis was performed to identify key cells and investigate the dynamic expression of potential biomarkers. At last, qRT-PCR, immunofluorescence and immunohistochemistry were carried out to verify these findings. A total of 104 candidate genes were identified, enriched in pathways like "wound healing", "PI3K-Akt signaling", and "neuroactive ligand-receptor interaction". The 3 potential biomarkers (Arg1, Mmp3, and Plaur) were validated in validation set, showing significant upregulation in SCI. And Arg1 and Plaur were further validated in vivo. The murine potential biomarkers were converted to the corresponding human potential biomarkers, namely ARG1, MMP3, and PLAUR. These potential biomarkers localized to extracellular regions or the nucleus and exhibited tissue-specific expression (e.g., ARG1 in the right lobe of the liver). Drug predictions showed ARG1 linked to dequalinium. The scRNA-seq analysis identified that monocytes and endothelial cells were key cells, with Arg1and Plaur dynamically expressed during differentiation. qRT-PCR showed that Arg1 and Plaur levels peaked at 7 days post-injury. This study identified ARG1and PLAUR as SCI potential biomarkers and underscored monocytes and endothelial cells as critical players in SCI pathology. The findings provide insights into molecular mechanisms, regulatory networks, and therapeutic targets for SCI.