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Updated: Aug 23, 2025
Development of Compendium for Esophageal Squamous Cell Carcinoma
Published on: April 12, 2024
Bioinformatics-based identification of miRNAs, mRNA, and regulatory signaling pathways involved in esophageal
Nahid Askari1, Morteza Hadizadeh2
1Department of Biotechnology, Institute of Sciences and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
Aim:
The current study analyzed the miRNA microarray dataset (GSE66274) and gene expression microarray dataset (GSE38129) with similar samples to achieve a better understanding of miRNA-mRNA interactions.
Background:
The most common form of esophageal cancer is esophageal squamous cell carcinoma (ESCC). While, miRNAs are well recognized as having a critical regulatory role in human cancer, their responsibilities and mechanisms of miRNA-mRNA in ESCC are unknown.
Methods:
Differentially expressed miRNAs (DEmiRNAs) and mRNAs (DEmRNAs) were identified using the LIMMA package in R. In total, 478 DEmRNA (224 upregulated and 254 downregulated) and 39 DEmiRNA (15 upregulated and 24 downregulated) were screened. The RNAInter database analyzed miRNA-mRNA interactions; then, the miRNA-mRNA network was visualized by Cytoscape software. ClusterProfiler packages were used to perform gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses for DEmRNA as targets of DEmiRNAs.
Results:
KEGG pathway analysis indicated that the p53 signaling pathway, ECM-receptor interaction, and AGE-RAGE signaling pathway were significant. Cellular response to amino acid stimulus, negative regulation of apoptotic signaling pathway, and endoderm formation were most prevalent in the biological process category. Additionally, the collagen-containing extracellular matrix, actomyosin complex collagen trimers, basement membrane, and extracellular matrix structural constituent were more enriched.
Conclusion:
Overall, the present survey provides evidence that could support the prognosis of esophageal tumors in the future.
Insights
This study investigated microRNA-messenger RNA interactions in esophageal squamous cell carcinoma (ESCC) using gene and miRNA expression data. Key pathways like p53 signaling and extracellular matrix interactions were identified, offering insights for future ESCC prognosis.
Area of Science:
- Oncology
- Molecular Biology
- Bioinformatics
Background:
- Esophageal squamous cell carcinoma (ESCC) is a prevalent cancer.
- MicroRNAs (miRNAs) play a regulatory role in human cancers.
- The specific roles of miRNA-mRNA interactions in ESCC remain largely unknown.
Purpose of the Study:
- To elucidate miRNA-mRNA interactions in ESCC.
- To identify key molecular pathways involved in ESCC pathogenesis.
- To provide evidence for improved ESCC tumor prognosis.
Main Methods:
- Analysis of miRNA (GSE66274) and gene expression (GSE38129) datasets.
- Identification of differentially expressed miRNAs (DEmiRNAs) and mRNAs (DEmRNAs) using LIMMA.
- Construction and visualization of miRNA-mRNA interaction networks using RNAInter and Cytoscape.
- Gene Ontology (GO) and KEGG pathway enrichment analyses using ClusterProfiler.
Main Results:
- Identified 39 DEmiRNAs and 478 DEmRNAs.
- Significant pathways include p53 signaling, ECM-receptor interaction, and AGE-RAGE signaling.
- Enriched biological processes involve cellular response to amino acid stimulus and apoptotic signaling.
- Key molecular components include extracellular matrix and collagen structures.
Conclusions:
- The study reveals significant miRNA-mRNA interactions in ESCC.
- Identified pathways and molecular components offer potential targets for understanding ESCC.
- Findings may contribute to the future prognosis of esophageal tumors.
