Multi-Transcriptomic Analysis Reveals GSC-Driven MES-Like Differentiation via EMT in GBM Cell–Cell Communication
Abstract
:1. Background
2. Materials and Methods
2.1. Data Source and Processing
2.2. Cell–Cell Interaction Analysis
2.3. Functional Enrichment Analysis
2.4. Processing of GBM Spatial Transcriptome Sequencing Data
2.5. Cell Lines and Cell Culture
2.6. SiRNA Transfection
2.7. Immunoblotting
2.8. Statistical Analysis
3. Results
3.1. Initial Clustering and Identification of Cell Types in GBM
3.2. Overview of the Communication Network in GBM
3.3. Cell–Cell Communication Strength Across 10 Cell Groups
3.4. The Cell Communication Pattern of GSCs Is Mostly Related to EMT
3.5. Spatial Co-Localization of EMT and GSCs in GBM
3.6. Elevated Expression of EMT-Associated Genes in GBM
3.7. Elevated Expression of EMT-Associated Genes Correlates with Poor Prognosis
3.8. GSCs Exhibit Pronounced Overexpression of EMT-Associated Gene Signature in GBM
3.9. EMT-Related Genes Are More Enriched in MES-like GSCs
3.10. Clinical Significance: Worse Prognosis Associated with High MES-like Signature Expression in Brain Tumor Patients
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
GBM | Glioblastoma |
CNS | Central nervous system |
SoC | Standard of care |
GSCs | Glioma stem cells |
TME | Tumor microenvironment |
scRNA-seq | Single-cell RNA sequencing |
EMT | Epithelial–mesenchymal transition |
GEO | Gene Expression Omnibus |
NCBI | National Center for Biotechnology Information |
PCA | Principal component analysis |
DGCs | Differentiated glioma cells |
IGV | Integrative Genomics Viewer |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
GSEA | Gene set enrichment analysis |
ssGSEA | Single-sample GSEA |
OPCs | Oligodendrocyte precursor cells |
PTN | Pleiotrophin |
MK | Midkine |
SPP1 | Secreted phosphoprotein 1 |
FGF | Fibroblast growth factor |
CSF | Colony-stimulating factor |
PROS | Prosaposin |
TGF-β | Transforming growth factor beta |
VEGF | Vascular endothelial growth factor |
LIFR | Leukemia inhibitory factor receptor |
CALCR | Calcitonin receptor |
NES | Normalized enrichment score |
FDR | False discovery rate |
TCGA | The Cancer Genome Atlas |
CGGA | Chinese Glioma Genome Atlas |
OPC-like | Oligodendrocyte precursor cell-like |
NPC-like | Neural progenitor cell-like |
AC-like | Astrocyte-like |
MES-like | Mesenchymal-like |
IQR | Interquartile range |
PN | Proneural |
CL | Classical |
MDSCs | Myeloid-derived suppressor cells |
GAMs | Glioma-associated microglia/macrophages |
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Data | Species | GPL | Data Type | Information |
---|---|---|---|---|
GSE84465 | Homo sapiens | GPL18573 | scRNA-seq | Examination of cell types in human GBM samples |
GSE129438 | Homo sapiens | GPL11154 | CHIP-seq | H3K27ac ChIP-seq of 2 pairs of GSCs and matched DGCs |
GSE131928 | Homo sapiens | GPL18573 | scRNA-seq | 24,131 single cells from 28 patients with GBM |
Antibodies | Source | Cat No. |
---|---|---|
SOX2 polyclonal antibody | Proteintech | 11064-1-AP |
GFAP polyclonal antibody | Proteintech | 16825-1-AP |
SURVIVIN (BIRC5) polyclonal antibody | Proteintech | 10508-1-AP |
Vimentin (VIM) polyclonal antibody | Proteintech | 10366-1-AP |
Beta catenin polyclonal antibody | Proteintech | 51067-2-AP |
SNAI2/SLUG polyclonal antibody | Proteintech | 12129-1-AP |
Alpha tubulin polyclonal antibody | Proteintech | 11224-1-AP |
CD44 polyclonal antibody | Proteintech | 15675-1-AP |
ZEB1 polyclonal antibody | Proteintech | 21544-1-AP |
ZO-1 polyclonal antibody | Proteintech | 21773-1-AP |
MMP-9 (N-terminal) polyclonal antibody | Proteintech | 10375-2-AP |
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Wu, W.; Zhang, P.; Li, D.; He, K. Multi-Transcriptomic Analysis Reveals GSC-Driven MES-Like Differentiation via EMT in GBM Cell–Cell Communication. Biomedicines 2025, 13, 1304. https://doi.org/10.3390/biomedicines13061304
Wu W, Zhang P, Li D, He K. Multi-Transcriptomic Analysis Reveals GSC-Driven MES-Like Differentiation via EMT in GBM Cell–Cell Communication. Biomedicines. 2025; 13(6):1304. https://doi.org/10.3390/biomedicines13061304
Chicago/Turabian StyleWu, Weichi, Po Zhang, Dongsheng Li, and Kejun He. 2025. "Multi-Transcriptomic Analysis Reveals GSC-Driven MES-Like Differentiation via EMT in GBM Cell–Cell Communication" Biomedicines 13, no. 6: 1304. https://doi.org/10.3390/biomedicines13061304
APA StyleWu, W., Zhang, P., Li, D., & He, K. (2025). Multi-Transcriptomic Analysis Reveals GSC-Driven MES-Like Differentiation via EMT in GBM Cell–Cell Communication. Biomedicines, 13(6), 1304. https://doi.org/10.3390/biomedicines13061304