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Updated: Dec 17, 2025
Identification of Circular RNAs using RNA Sequencing
Published on: November 14, 2019
Expression profile and bioinformatics analysis of circular RNAs in acute ischemic stroke in a South Chinese Han
Shenghua Li1, Lan Chen2, Chen Xu1
1Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.
Insights
Circular RNAs (circRNAs) are dysregulated in acute ischemic stroke (AIS). Specific circRNAs, hsa_circ_0000607 and hsa_circ_0002465, show potential as diagnostic biomarkers for AIS.
Area of Science:
- Molecular Biology
- Genomics
- Biochemistry
Background:
- Circular RNAs (circRNAs) are increasingly recognized for their roles in normal development and disease pathogenesis.
- The expression and function of circRNAs in acute ischemic stroke (AIS) within the South Chinese Han population remain largely uncharacterized.
Purpose of the Study:
- To investigate the differential expression patterns of circRNAs in AIS patients compared to healthy controls.
- To identify potential circRNA biomarkers for the diagnosis of AIS.
- To explore the functional roles and regulatory networks of differentially expressed circRNAs in AIS pathogenesis.
Main Methods:
- RNA sequencing (RNA-seq) was performed on samples from 3 AIS patients and 3 healthy controls.
- CircRNAs were identified using CIRI2 and Find_circ software, with expression validated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR).
- Bioinformatic analyses included gene ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and prediction of circRNA-miRNA-mRNA interaction networks.
Main Results:
- A total of 2270 differentially expressed circRNAs were identified between AIS patients and controls, with 659 upregulated and 1611 downregulated.
- Bioinformatic analysis linked these circRNAs to key biological processes such as endocytosis, energy metabolism, apoptosis, and signaling pathways (FoxO, neurotrophin, VEGF).
- hsa_circ_0000607 and hsa_circ_0002465 demonstrated significant potential as diagnostic biomarkers for AIS, with Area Under Curve (AUC) values of 0.75 and 0.69, respectively.
Conclusions:
- Numerous circRNAs are dysregulated in AIS, suggesting their involvement in the disease's pathology.
- hsa_circ_0000607 and hsa_circ_0002465 are promising diagnostic biomarkers for AIS.
- hsa_circ_0000607 may play a critical role in AIS pathogenesis by regulating the miR-337-3p/Bcl2 axis.
Abstract:
Recent studies have found that circular RNAs (circRNAs) play crucial roles not only in the normal growth and the development of different tissues and organs but also in the pathogenesis and progression of various disorders. However, the expression patterns and the function of circRNAs in acute ischemic stroke (AIS) in the South Chinese Han population are unclear. In the present study, RNA sequencing (RNA-seq) data was generated from 3 AIS patients and 3 healthy controls. The circRNAs were detected and identified by CIRI2 and Find_circ software. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analyses were used to detect the expression of circRNAs. Meanwhile, the potential diagnostic value of the selected circRNAs for AIS was assessed by generating receiver operating characteristic (ROC) curve with area under curve (AUC). The bioinformatic analysis of the host genes of differentially expressed (DE) circRNAs was performed by gene ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, KOBAS for pathway analysis and regulatory network analysis. miRNA-circRNA and miRNA-mRNA interactions were predicted by using TargetScan, miRanda and starBase. CircRNA-miRNA-mRNA interaction networks were created with Cytoscape. Our result showed that there were 2270 DE circRNAs between AIS patients and healthy controls. Among them, 659 were found upregulated and 1611 were downregulated. Bioinformatic analysis showed that the DE circRNAs were related to the following biological processes: endocytosis, energy metabolism, apoptosis, FoxO signaling pathway, platelet activation, neurotrophin signaling pathway and VEGF signaling pathway, which may be associated with the pathological of AIS. Three randomly selected circRNAs were successfully validated by qRT-PCR. The results show that hsa_circ_0005548 was significantly upregulated, while hsa_circ_0000607 and hsa_circ_0002465 were significantly downregulated in AIS. Furthermore, the AUC values for hsa_circ_005548, hsa_circ_0000607 and hsa_circ_0002465 were 0.51, 0.75 and 0.69, respectively, suggesting that hsa_circ_0000607 and hsa_circ_0002465 could be potential biomarkers for AIS. In addition, Bcl2 was predicted to be a direct target of miR-337-3p, and hsa_circRNA_0000607 was predicted to act as a sponge for miR-337-3p. Thus, hsa_circ_0000607 may be involved in AIS by regulating the miR-337-3p/Bcl2 axis. Collectively, our findings indicate that numerous dysregulated circRNAs may play pivotal functional roles in AIS and hsa_circ_0000607 may play a crucial role in the pathogenesis and progression of AIS by regulating the miR-337-3p/Bcl2 axis.
