Analysis of Circular RNA Expression Profile in HEK 293T Cells Exposed to Ionizing Radiation

Abstract

Radiation therapy is one of the most common cancer treatments. It is important to understand how cells respond to ionizing radiation (IR) to improve therapeutic efficacy. Circular RNAs (circRNAs) recently have been found to regulate a variety of cellular processes. However, it is poorly defined that their expression pattern and their identity in cells following IR exposure. Here, we performed high-throughput sequencing and comprehensive analysis of circRNA expression in human embryonic kidney (HEK) 293T cells before and after irradiation. We identified totally 5592 circRNAs and discovered 1038 new circRNAs. We found 158 circRNAs with significantly differential expression after IR exposure. Among them, there were 61 upregulated and 97 downregulated circRNAs. Using Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway, and circRNA-microRNAmessenger RNA network analyses, we found the differentially expressed circRNAs might be involved in the signal pathways of oxidative phosphorylation, epithelial growth factor receptor (EGFR) tyrosine kinase inhibitor resistance, and mammalian target of rapamycin (mTOR) signaling.

Experimental Models for the Study of Central Nervous System Infection by SARS-CoV-2

“…This cell line is a variant of the HEK 293 lineage, which was isolated from kidney epithelial cells extracted from human embryos ( 49 ). Both lines are widely used in research due to their high transfectability, gene expression, and production of proteins or recombinant retrovirus ( 23 , 49 , 50 ). The HEK 293T variant expresses the T SV-40 antigen, which enables the amplification of transfected plasmids containing the SV40 origin of replication and thus considerably increases the expression levels of desired gene products ( 50 ).…”

“…Both lines are widely used in research due to their high transfectability, gene expression, and production of proteins or recombinant retrovirus ( 23 , 49 , 50 ). The HEK 293T variant expresses the T SV-40 antigen, which enables the amplification of transfected plasmids containing the SV40 origin of replication and thus considerably increases the expression levels of desired gene products ( 50 ). These cells have also previously been used in studies of other such viruses as herpes simplex virus, SARS-CoV, and even CoV pseudovirions ( 34 , 51 – 53 ).…”

Role of non-coding RNAs and RNA modifiers in cancer therapy resistance

“…In GBM, circ-AKT3 is reported to encode AKT3-174aa, a novel tumor suppressor protein, and enhance radiation sensitivity cells by negatively regulating the PI3K/Akt pathway [207]. Besides, high-throughput sequencing and bioinformatic analysis reveals significant circRNAs expression in cancer radioresistance, like hsa_circ_0004015 [208], circRNA_001059 and circRNA_000167 [209] circATP8B4 [210], hsa_circ_0000734 [211], etc., which establishes the circRNA-miRNA-target gene interaction network. One circRNA can target various miRNAs, and one miRNA can also suppress its downstream genes.…”

“…CircATP8B4 is one of the circRNAs in extracellular vesicles isolated from radioresistant glioma cells and induces therapy resistance by sponging U251 miR-766 [210]. Hsa_circ_0000734 is discovered to modulate hsa-miR-432-5p and hsa-miR-124-5p, which can further control the expression of target genes [211]. As a result, circRNAs play a comprehensive role in tumor radiotherapy, which provides some new insights on therapeutic approaches.…”

Functions and mechanisms of circular RNAs in cancer radiotherapy and chemotherapy resistance

“…It was identified that 61 circRNAs are upregulated and 97 are downregulated in human embryonic kidney (HEK) 293 T cells following radiation. The circRNA-miRNA-mRNA network analysis revealed that the altered circRNAs were suggested to be involved in EGFR and mTOR signaling, which is worth further studies in cancer cells [154]. Duo et al identified 76 upregulated and 77 downregulated circRNAs in irradiated HeLa cells.…”