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Updated: Dec 10, 2025
Using Microarrays to Interrogate Microenvironmental Impact on Cellular Phenotypes in Cancer
Published on: May 21, 2019
Microarray data analysis reveals gene expression changes in response to ionizing radiation in MCF7 human breast
Jing Bai1, Youzhen Luo1, Shengchu Zhang2
1Department of Gynaecology, The First College of Clinical Medical Sciences, China Three Gorges University, Yichang Central People's Hospital, Yichang, 443000, Hubei, China.
Background:
The aim of this study was to identify potential therapeutic target genes for breast cancer (BC) by the investigation of gene expression changes after ionizing radiation (IR) in BC cells. Gene expression profile GSE21748, including BC cell line MCF-7 samples at different time points after IR treatment, were downloaded from Gene Expression Omnibus. Differentially expressed genes (DEGs) were identified in different time points following IR compared with cell samples before IR, respectively. Gene ontology functions and The Kyoto Encyclopedia of Genes and Genomes pathways of the overlapping DEGs were enriched using DAVID. Transcription factor (TFs)-encoding genes were identified from the overlapping DEGs, followed by construction of transcriptional regulatory network and co-expression network.
Results:
A total of 864 overlapping DEGs were identified, which were significantly enriched in regulation of cell proliferation and apoptosis, and cell cycle process. We found that FOXD1, STAT6, XBP1, STAT2, LMO2, TFAP4, STAT3, STAT1 were hub nodes in the transcriptional regulatory network of the overlapping DEGs. The co-expression network of target genes regulated by STAT3, STAT1, STAT6 and STAT2 included some key genes such as BCL2L1.
Conclusion:
STAT1, STAT2, STAT3, STAT6, XBP1, BCL2L1, CYB5D2, ESCO2, and PARP2 were significantly affected by IR and they may be used as therapeutic gene targets in the treatment of BC.
Insights
Ionizing radiation (IR) affects gene expression in breast cancer (BC) cells. Key genes like STAT1, STAT2, STAT3, and STAT6 were identified as potential therapeutic targets for BC treatment.
Area of Science:
- Genomics
- Molecular Biology
- Cancer Research
Background:
- Investigated gene expression changes in breast cancer (BC) cells following ionizing radiation (IR).
- Utilized gene expression profile GSE21748 from the Gene Expression Omnibus database, including MCF-7 cell line samples.
- Focused on identifying differentially expressed genes (DEGs) at various time points post-IR.
Purpose of the Study:
- To identify potential therapeutic target genes for breast cancer (BC).
- To understand the molecular mechanisms underlying BC response to ionizing radiation (IR).
- To construct transcriptional regulatory and co-expression networks for DEGs.
Main Methods:
- Downloaded and analyzed gene expression data (GSE21748) from the Gene Expression Omnibus.
- Identified differentially expressed genes (DEGs) by comparing IR-treated samples with pre-IR samples.
- Utilized DAVID for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis.
- Constructed transcriptional regulatory and co-expression networks using identified transcription factors (TFs) and DEGs.
Main Results:
- Identified 864 overlapping DEGs significantly enriched in cell proliferation, apoptosis, and cell cycle regulation.
- FOXD1, STAT6, XBP1, STAT2, LMO2, TFAP4, STAT3, and STAT1 emerged as hub nodes in the transcriptional regulatory network.
- Co-expression network analysis revealed key genes like BCL2L1 regulated by STAT3, STAT1, STAT6, and STAT2.
Conclusions:
- STAT1, STAT2, STAT3, STAT6, XBP1, BCL2L1, CYB5D2, ESCO2, and PARP2 were significantly impacted by IR.
- These identified genes represent potential therapeutic targets for breast cancer (BC) treatment.
