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Updated: Nov 14, 2025
Identification of Circular RNAs using RNA Sequencing
Published on: November 14, 2019
Identification of differentially expressed circular RNAs associated with thymoma
Qingjun Wu1, Xuanmei Luo2, Hexin Li3
1Department of thoracic surgery, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.
Background:
Thymomas and thymic carcinomas are the most common tumor types among anterior mediastinal lesions. However, the relationship between molecular aberrations and thymoma patients are poorly understood, especially abnormal changes in the expression profiles of circRNAs. The purpose of the present study was to investigate the expression profiles of circRNAs in thymoma patients and their possible roles in the pathogenesis of thymoma.
Methods:
Diseased tissues and surrounding normal thymic tissues in two thymoma patients were collected for circRNA sequencing. The top four upregulated circRNAs were selected as candidates and further validated with RT-PCR in 20 thymoma patients. Gene ontology and signal transduction network analyses of circRNA-related mRNAs were performed to analyze the functional properties. Survival analysis of their parental genes were also carried out to evaluate the clinical value of differentially expressed circRNA.
Results:
A total of 73 circRNAs were differentially expressed in thymoma tissues using high-throughput sequencing. Among these circRNAs, hsa_circ_0001173, hsa_circ_0007291, hsa_circ_0003550, and hsa_circ_0001947 were significantly upregulated in thymoma tissues compared with normal thymic tissues. We identified that these four circRNA-related mRNAs were involved in cell-cell adhesion, MAPK pathways, and TNF pathway, which may contribute to the pathological immune disorder in thymoma. Finally, we also found that SCAP (hsa_circ_0007291 parental gene) and AFF2 (hsa_circ_0001947 parental gene) were all significantly related with progression-free survival (PFS) of thymoma patients in a Kaplan-Meier plot (p-value <0.05).
Conclusions:
The expression levels of hsa_circ_0001173, hsa_circ_0007291, hsa_circ_0003550, and hsa_circ_0001947 were significantly upregulated and positively correlated with immune imbalance in thymoma patients.
Insights
This study investigated circular RNAs (circRNAs) in thymoma, finding four significantly upregulated circRNAs linked to immune imbalance. These circRNAs and their parental genes show potential as biomarkers for thymoma progression and patient survival.
Area of Science:
- Oncology
- Molecular Biology
- Genomics
Background:
- Thymomas and thymic carcinomas are common anterior mediastinal tumors.
- Molecular aberrations in thymoma, particularly circRNA expression, are poorly understood.
- Investigating circRNA profiles can elucidate thymoma pathogenesis.
Purpose of the Study:
- To investigate circRNA expression profiles in thymoma patients.
- To explore the potential roles of circRNAs in thymoma pathogenesis.
- To identify circRNAs as potential diagnostic or prognostic markers.
Main Methods:
- circRNA sequencing of thymoma tissues and adjacent normal tissues.
- Validation of top upregulated circRNAs using RT-PCR in a larger cohort.
- Gene ontology, pathway analysis, and survival analysis of circRNA-related genes.
Main Results:
- 73 differentially expressed circRNAs identified in thymoma tissues.
- Four circRNAs (hsa_circ_0001173, hsa_circ_0007291, hsa_circ_0003550, hsa_circ_0001947) were significantly upregulated.
- Upregulated circRNAs are linked to cell-cell adhesion, MAPK, and TNF pathways, suggesting immune dysregulation.
- Parental genes SCAP and AFF2 correlated significantly with progression-free survival.
Conclusions:
- Specific circRNAs are significantly upregulated in thymoma.
- These circRNAs correlate with immune imbalance in thymoma patients.
- Identified circRNAs and their parental genes may serve as prognostic indicators for thymoma.
