Identification of key genes of intestinal stem cells and differentiated cells in radiation-induced intestinal injury

Abstract: Objective: To examine changes in the expression profiles of intestinal stem cells (ISCs) and their differentiated cells during radiation-induced intestinal injury (RIII) and to screen the key genes. Methods: The Seurat package was used to perform cluster analysis and differential expression analysis on a single-cell sequencing dataset (GSE165318) to identify differentially expressed genes in each cell type. The TCseq package analyzed the expression trend over time. Key genes were identified by intersecting up-regulated genes with specific trend gene clusters across the five cell types. The clusterProfiler package and STRING database were used for Gene Ontology (GO) enrichment analysis and PPI network analysis of key genes. A mouse model of RIII was established via abdominal irradiation with 12 Gy of 60Co γ-rays. Intestinal tissues were collected at 0, 3, and 7 days post-irradiation in control and treatment groups. Key genes were verified using Real-time quantitative PCR (RT-qPCR). Results: Twelve intestinal cell types were identified, and the key gene Mmp8 was found in ISCs and their differentiated cells. Additionally, the expression of 15 Mmp family members peaked on the 3rd day after irradiation, with heterogeneous expression across different cell types. PPI network analysis revealed that Mmp3, Mmp7, Mmp8, Mmp9, and Mmp11 are central in the regulatory network. The differential expression of Mmp8, Mmp9, Mmp13, Mmp19, and Mmp25 was validated by RT-qPCR. Conclusion: Mmp family plays an important role in radiation-induced intestinal injury and repair, among which Mmp8, Mmp9, Mmp13, Mmp19, and Mmp25 may be potential therapeutic targets for RIII.