Single-cell transcriptome reveals features of key factors and cellular communication in spinal cord injury
10.3760/cma.j.cn121113-20240514-00293
- VernacularTitle:单细胞测序分析脊髓损伤修复的关键基因和细胞通讯
- Author:
Yan AN
1
;
Xiang ZHU
;
Bo WANG
;
Lin ZHANG
;
Shiyan YU
Author Information
1. 首都医科大学附属北京积水潭医院脊柱外科,北京 100035
- Publication Type:Journal Article
- Keywords:
Spinal cord injuries;
Genes;
RNA-seq;
High-throughput nucleotide sequencing;
Cell communication
- From:
Chinese Journal of Orthopaedics
2025;45(5):302-309
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To investigate key genes and cellular communication involved in spinal cord injury (SCI) repair using transcriptome sequencing and single-cell sequencing analysis.Methods:Two transcriptome sequencing datasets related to SCI and one single-cell sequencing dataset were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) in the two transcriptome sequencing datasets were analyzed using the limma package in R, followed by cross-analysis to identify common DEGs. Functional enrichment analysis of DEGs was performed using the DAVID database for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Hub genes in the protein-protein interaction (PPI) network were identified using the cytoHubba plugin in Cytoscape. Single-cell sequencing data were analyzed using the Seurat package in R. Principal Component Analysis (PCA) was applied for dimensionality reduction, and t-distributed Stochastic Neighbor Embedding (t-SNE) was used for visualization. Cellular communication between different cell groups was analyzed using the CellChat package.Results:Differential analysis of transcriptome sequencing data identified 98 common DEGs. GO and KEGG enrichment analysis highlighted biological processes such as wound healing, macrophage activation, and immune response-related cell activation. The PPI network predicted 10 hub genes: ITGAM, TGFB1, CCL2, ICAM1, CD44, FN1, TIMP1, TLR2, ITGB2, and LGALS3. Single-cell sequencing analysis identified six distinct cell populations, including astrocytes, neurons, and fibroblasts. Cellular communication analysis revealed key signaling pathways between cell subpopulations, including SPP1- (ITGAV+ITGB1), SPP1- (ITGA5+ITGB1), TNF-TNFRSF1A transmission pathway, etc.Conclusions:During SCI repair, astrocytes receive signals from fibroblasts, monocytes, and neurons via the SPP1 pathway, while astrocytes and neurons receive signals from monocytes through the TNF pathway. These findings provide critical insights into the molecular mechanisms underlying SCI repair and offer a foundation for future research.
