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Updated: Jan 10, 2026
Isolating, Sequencing and Analyzing Extracellular MicroRNAs from Human Mesenchymal Stem Cells
Published on: March 8, 2019
Analysis of key immune genes in mesenchymal stem cells in a 3D environment
Haojiang Li1, Jianfei Gao1, Ren Zhang1
1Foot and Ankle Surgery Ward of The Second People's Hospital of Changzhi No. 82, Heping West Street, Luzhou District, Changzhi 046000, Shanxi, China.
Objective:
The aim of this study was to identify the different immune-related genes (DIRGs) of mesenchymal stem cells (MSCs) in three-dimensional (3D) vs. two-dimensional (3D) environment.
Materials And Methods:
The gene expression dataset GSE52896 was downloaded from the Gene Expression Omnibus (GEO) database. We obtained immune-related genes from the ImmPort database. The array was processed with the R language to obtain differentially expressed genes (DEGs). A protein-protein interaction (PPI) network was constructed with the STRING database and analyzed with Cytoscape. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis data were performed with DAVID (https://davidbioinformatics.nih.gov/). We constructed a least absolute shrinkage and selection operator (LASSO) regression model and multiple support vector machine - recursive feature elimination (mSVM-RFE) model to identify the key DIRGs in cells growing in 3D culture. The performance of the key genes was validated in the GSE58919 dataset. Western blot analysis was performed to verify the expression of one key gene, Cysteine and Glycine Rich Protein 1 (CSRP1). Key immune-related genes were identified using CIBERSORT (https://cibersortx.stanford.edu/).
Results:
A total of 446 DEGs were screened under two different culture conditions (2D and 3D), and 65 DEGs were identified. GO analysis revealed changes in inflammatory response, extracellular region, and protein binding. KEGG enrichment analysis showed that the DEGs were enriched in pathways involved in cytokine-cytokine receptor interactions, viral protein interactions with cytokines and cytokine receptors and the TNF signaling pathway. Seven key genes were obtained from the intersection of the outputs of the LASSO and mSVM-RFE algorithms. The expression of the seven key genes was verified in the GSE52896 dataset. Western blot (WB) confirmed the alteration of CSRP1 expression under different culture conditions.
Conclusion:
Stem cells showed significant changes in immune response gene expression under 3D culture conditions. CSRP1 plays essential roles in MSC immunomodulation.
