Identification of key autophagy‑related genes and pathways in spinal cord injury

Scientific Reports, 2024 · DOI: 10.1038/s41598-024-56683-1 · Published: March 9, 2024

Spinal Cord Injury Genetics Bioinformatics

Simple Explanation

This study explores the role of autophagy in spinal cord injury (SCI) by identifying key autophagy-related genes and pathways using bioinformatics methods. The GSE132242 dataset, consisting of control and SCI samples, was analyzed to screen differentially expressed genes (DEGs), which were then intersected with autophagy-related genes. Protein-protein interaction (PPI) analysis was conducted to identify interaction genes, and hub genes were screened using the cytoHubba plug-in. The GSE5296 dataset was used to verify the reliability of the hub genes.

Study Duration

Not specified

Participants

GSE132242 dataset: four SCI mouse samples and four spinal cord tissue samples from a sham operation group. GSE5296 dataset: three SCI model samples and three spinal cord tissue samples from a sham operation group.

Evidence Level

Level 5: Bioinformatics analysis

Key Findings

1
A total of 129 autophagy-related DEGs were identified, including 126 up-regulated and 3 down-regulated genes.
2
GO and KEGG pathway enrichment analysis showed that these genes were mainly involved in cell apoptosis, angiogenesis, IL-1 production, inflammatory reactions, the TNF signaling pathway, and the p53 signaling pathway.
3
PPI identified 10 hub genes, including CCL2, TGFB1, PTGS2, FN1, HGF, MYC, IGF1, CD44, CXCR4, and SERPINEL1. The GSE5296 dataset revealed that only CD44 and TGFB1 showed significant differences.

Research Summary

This study identified 129 autophagy-related genes that might play a role in SCI, providing new targets for future research and offering new perspectives on the pathogenesis of SCI. The results of the GO analysis revealed that the 129 autophagy-related DEGs mainly functioned in the cytoplasm, nucleus, and cytosol and were involved in apoptosis, angiogenesis, and the regulation of IL-1β production and the inflammatory response. After multiple validations, the results suggested that CD44 and TGFB1 as potential research and treatment targets for autophagy after SCI.

Practical Implications

Therapeutic Targets

CD44 and TGFB1 were identified as potentially important genes in the autophagy process after SCI, offering new therapeutic targets.

Understanding SCI Pathogenesis

The identification of key autophagy-related genes and pathways provides new insights into the molecular mechanisms underlying SCI.

Future Research Directions

The identified hub genes and pathways can be further investigated to develop targeted interventions for SCI.

Study Limitations

1
Limited sample size in the analyzed dataset.
2
Potential errors in the validation dataset due to the publication date and technical reasons.
3
Lack of in vivo and in vitro experiments to further study the potential mechanism of the selected hub genes.

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