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Updated: Aug 5, 2025
Identification of Circular RNAs using RNA Sequencing
Published on: November 14, 2019
Identification of Key Differentially Expressed mRNAs, miRNAs, lncRNAs, and circRNAs for Xp11 Translocation Renal Cell
Changqi Deng1, Chengcheng Wei1, Yaxin Hou2
1Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China.
Abstract:
We carried out whole transcriptome sequencing (WTS) on the tumor and the matching adjacent normal tissues from five patients having Xp11 translocation renal cell carcinoma (RCC). This was performed in terms of obtaining more understanding of the genomic panorama and molecular basis of this cancer. To examine gene-regulatory networks in XP11 translocation RCC, variance expression analysis was carried out, followed by functional enrichment analysis. Gene Expression Omnibus (GEO) of Xp11 translocation RCC data was used to validate the results. As per inclusion criteria, a total of 1886 differentially expressed mRNAs (DEmRNAs), 56 differentially expressed miRNAs (DEmiRNAs), 223 differentially expressed lncRNAs (DElncRNAs), and 1764 differentially expressed circRNAs (DEcircRNAs) were found. KEGG enrichment study of DEmiRNA, DElncRNA, and DEcircRNA target genes identified the function of protein processing in the endoplasmic reticulum, lysosome, and neutrophil-mediated immunity. Three subnetwork modules integrated from the PPI network also revealed the genes involved in protein processing in the endoplasmic reticulum, lysosome, and protein degradation processes, which may regulate the Xp11 translocation RCC process. The ceRNA complex network was created by Cytoscape, which included three upregulated circRNAs, five upregulated lncRNAs, 24 upregulated mRNAs, and two downregulated miRNAs (hsa-let-7d-5p and hsa-miR-433-3p). The genes as a prominent component of the complex ceRNA network may be key factors in the pathogenesis of Xp11 translocation RCC. Our findings clarified the genomic and transcriptional complexity of Xp11 translocation RCC while also pointing to possible new targets for Xp11 translocation RCC characterization.
Insights
Whole transcriptome sequencing revealed key molecular differences in Xp11 translocation renal cell carcinoma (RCC). This study identified novel gene regulatory networks and potential therapeutic targets for this rare kidney cancer.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- Xp11 translocation renal cell carcinoma (RCC) is a rare subtype requiring deeper molecular understanding.
- Genomic and transcriptional complexity of Xp11 translocation RCC remains incompletely characterized.
Purpose of the Study:
- To elucidate the genomic landscape and molecular basis of Xp11 translocation RCC.
- To identify gene-regulatory networks and potential therapeutic targets.
Main Methods:
- Whole transcriptome sequencing (WTS) of tumor and adjacent normal tissues from five patients.
- Differential expression analysis of mRNAs, miRNAs, lncRNAs, and circRNAs.
- Functional enrichment analysis (KEGG) and protein-protein interaction (PPI) network construction.
- Validation using Gene Expression Omnibus (GEO) data.
Main Results:
- Identified 1886 DEmRNAs, 56 DEmiRNAs, 223 DElncRNAs, and 1764 DEcircRNAs.
- KEGG analysis highlighted protein processing in endoplasmic reticulum, lysosome, and neutrophil-mediated immunity.
- Constructed a ceRNA network implicating specific circRNAs, lncRNAs, mRNAs, and miRNAs in pathogenesis.
Conclusions:
- The study clarifies the transcriptional complexity of Xp11 translocation RCC.
- Identified key genes and regulatory networks involved in Xp11 translocation RCC pathogenesis.
- Potential novel targets for Xp11 translocation RCC characterization and treatment were proposed.
