Microarray data analysis reveals gene expression changes in response to ionizing radiation in MCF7 human breast cancer cells

Jing Bai,Youzhen Luo,Shengchu Zhang

doi:10.1186/s41065-020-00151-z

Abstract

BackgroundThe 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.ResultsA 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.ConclusionSTAT1, 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.

Highlights

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
Overlapping Differentially expressed genes (DEGs) analysis To determine the DEGs after IR treatment in breast cancer, a microarray dataset GSE2178, obtained from MCF7 human breast cancer cells, was downloaded from Gene Expression Omnibus (GEO)
Among the genes significantly affected by ionizing radiation, we discovered BCL2 Like 1 (BCL2L1), a gene involved in the regulation of apoptosis [37], and CYB5D2 that inhibits cell proliferation and has a putative tumor suppressor activity [38]

Summary

Introduction

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. Expressed genes (DEGs) were identified in different time points following IR compared with cell samples before IR, respectively. Transcription factor (TFs)-encoding genes were identified from the overlapping DEGs, followed by construction of transcriptional regulatory network and co-expression network. Free cancer cells can spread throughout the body by the blood or. IR is radiation that carries enough energy to make the electrons in atoms or molecules of a material into a free state, ionizing those atoms or molecules [7]. The idea behind IR therapy is that rapidly proliferating cancer cells are more sensitive to

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