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Updated: Jul 17, 2025
Identification of Circular RNAs using RNA Sequencing
Published on: November 14, 2019
Comprehensive analysis of circular RNAs in nasopharyngeal cancer
Si-Yu Zhu1, Xiao-Yi Wang2, Hui Xie3
1Department of Radiology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, 510060, Guangzhou, Guangdong, People's Republic of China.
Background:
Nasopharyngeal cancer (NPC) is a type of epithelial malignancy that is positive for Epstein-Barr virus (EBV) and affects several populations worldwide. Due to the high rates of relapse and metastasis following primary treatment, there is an urgent need to identify new candidates for NPC therapy. Recently, circular RNA (circRNA) has emerged as a promising target for cancer diagnosis and prevention.
Objective:
This study aimed to study the circRNAs enriched in NPC patients, and further analyze potential signaling pathways involved.
Methods:
A new bioinformatic tool named psirc was used to analyze RNA-sequencing datasets from NPC patients and normal specimens to study the NPC-enriched circRNAs.
Results:
We identified and quantified the full-length circRNA in these samples and found the top 10 enriched circRNAs in NPC patients compared to control samples. Furthermore, we selected the most enriched circRNA, circEEF1A1_E8B1, and studied its protein coding ability, microRNA and RNA-binding protein (RBP) binding capacity. We also constructed a protein-protein interaction (PPI) network for its binding proteins and extracted hub genes. Finally, we conducted survival analysis for these hub genes in head and neck cancer patients.
Conclusions:
In summary, our study has revealed the presence of previously unidentified circRNAs that are enriched in NPC patients. Through an analysis of their molecular functions, we have advanced our understanding of the potential role of circRNAs in NPC development.
Insights
This study identifies novel circular RNAs (circRNAs) enriched in nasopharyngeal cancer (NPC) patients. These findings advance understanding of circRNA roles in NPC development and potential therapeutic targets.
Area of Science:
- Oncology
- Molecular Biology
- Bioinformatics
Background:
- Nasopharyngeal cancer (NPC) is an epithelial malignancy associated with Epstein-Barr virus (EBV).
- High rates of NPC relapse and metastasis necessitate novel therapeutic strategies.
- Circular RNAs (circRNAs) show promise as diagnostic and therapeutic targets in cancer.
Purpose of the Study:
- To identify circRNAs specifically enriched in NPC patients.
- To analyze the potential signaling pathways involving these NPC-enriched circRNAs.
- To explore the molecular functions and therapeutic potential of identified circRNAs.
Main Methods:
- Utilized the psirc bioinformatic tool to analyze RNA-sequencing data from NPC and normal samples.
- Identified and quantified full-length circRNAs, focusing on the top 10 enriched in NPC.
- Investigated the protein-coding ability, microRNA/RNA-binding protein interactions, and constructed a protein-protein interaction network for a key circRNA (circEEF1A1_E8B1).
Main Results:
- Successfully identified and quantified circRNAs, pinpointing the top 10 enriched in NPC patients.
- Characterized circEEF1A1_E8B1 for its molecular interactions and identified associated hub genes.
- Performed survival analysis on hub genes within the context of head and neck cancers.
Conclusions:
- Revealed previously unidentified circRNAs significantly enriched in nasopharyngeal cancer.
- Advanced the understanding of circRNAs' molecular functions and their potential involvement in NPC pathogenesis.
- Highlighted the potential of circRNAs as novel targets for NPC diagnosis and therapy.
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