Whole Transcriptome-Based ceRNA Regulatory Network Analysis of Radiation-Induced Esophageal Epithelial Cell Injury

Abstract

Hongyu Lin,1,2,* Yahui Feng,1,3,* Hangfeng Liu,1 Jinkang Zhang,1,2 Xiaolin Zhang,1 Xue Ying,4 Yuhong Shi,1 Hao Tan,1,2 Wenling Tu1– 3 1The Second Affiliated Hospital of Chengdu Medical College, Nuclear Industry 416 Hospital, Chengdu, 610051, People’s Republic of China; 2School of Bioscience and Technology, Chengdu Medical College, Chengdu, 610500, People’s Republic of China; 3NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang, 621099, People’s Republic of China; 4Key Laboratory of Sichuan Province for Specific Structure of Small Molecule Drugs, School of Pharmacy, Chengdu Medical College, Chengdu, People’s Republic of China*These authors contributed equally to this workCorrespondence: Wenling Tu, The Second Affiliated Hospital of Chengdu Medical College, Nuclear Industry 416 Hospital, No. 4, Section 4, North Ring Road, Chenghua District, Chengdu, Sichuan Province, 610051, People’s Republic of China, Email [email protected] Hao Tan, The Second Affiliated Hospital of Chengdu Medical College, Nuclear Industry 416 Hospital, No. 4, Section 4, North Ring Road, Chenghua District, Chengdu, Sichuan Province, 610051, People’s Republic of China, Email [email protected]: Esophageal epithelial cells are essential for esophageal homeostasis and defense against harmful stimuli, but the mechanisms of radiation-induced injury in these cells are poorly understood. The competitive endogenous RNA (ceRNA) network, involved in various physiological processes and diseases, may also play a role in radiation-induced injury, although its mechanism remains unclear. This study aimed to investigate the effects of ionizing radiation on human esophageal epithelial cells and explore the role of the ceRNA network in this injury.Methods: Cellular phenotype experiments assessed the effects of ionizing radiation on human esophageal epithelial cells. Whole transcriptome sequencing (lncRNA, circRNA, miRNA, and mRNA) was performed on cells exposed to 0, 2, and 4 Gy radiation. Differentially expressed RNAs (dd-DERs) were identified through differential expression analysis and dose-dependent screening. A ceRNA network was constructed using co-expression analysis and binding site prediction. Real-time quantitative PCR validated the expression levels of selected dd-DERs, and gene set enrichment analysis explored affected pathways.Results: We identified 41 lncRNAs, 18 miRNAs, and 192 mRNAs as dose-dependent differentially expressed RNAs. A ceRNA network comprising 10 lncRNAs, 5 miRNAs, and 55 mRNAs was established. Real-time PCR confirmed the expression levels of 8 dd-DERs within the network. Gene set enrichment analysis showed that radiation disrupted channel activity, cell replication, repair, and immune response. Functional enrichment analysis revealed modulation of metabolic pathways, particularly involving UGT1A family members.Discussion: This study established a ceRNA network related to radiation-induced esophageal epithelial cell injury, advancing our understanding of its pathophysiology. The ceRNA network may mediate injury through metabolic pathway modulation. Future work should focus on elucidating specific ceRNA interactions and exploring therapeutic potential for mitigating radiation-induced esophageal injury.Keywords: ionizing radiation, esophageal epithelial cells, radiation-induced injury, whole transcriptome, competitive endogenous RNA network

Keywords

• ionizing radiation
• esophageal epithelial cells
• radiation-induced injury
• whole transcriptome
• competitive endogenous rna network