Construction and Comprehensive Analysis of the ceRNA Network to Reveal Key Genes for Benign Tracheal Stenosis

• Published in: Frontiers in genetics Vol. 13; p. 891741
• Main Authors: He, Yanpeng, Zou, Chunyan, Cai, Zhigang
• Format: Journal Article
• Language: English
• Published: Frontiers Media S.A 23-06-2022
• Subjects: benign tracheal stenosis; bioinformatics; competing endogenous RNA; differential analysis; Genetics; PPI; transcriptome sequencing
• ISSN: 1664-8021; 1664-8021
• DOI: 10.3389/fgene.2022.891741

Objective:
To explore the possible biological functions of the differentially expressed genes in patients with benign tracheal stenosis, and to provide a valuable molecular basis for investigating the pathogenesis of benign tracheal stenosis.
Method:
Whole transcriptome sequencing was performed on blood samples collected from patients with benign tracheal stenosis and normal controls. Differentially expressed mRNA, lncRNA, and circRNA were analyzed using the DESeq2 package. The protein interaction networks for differentially expressed mRNAs were constructed by STRING. The results of gene co-expression network analysis, Starbase database prediction, and differential gene expression were combined to construct a competing endogenous RNA network. The transcription factors of key genes were predicted using the Network Analyst database and a transcription factor-mRNA regulatory network was constructed. The classical pathways, intermolecular interaction networks, and upstream regulatory components of key genes were analyzed using Ingenuity Pathway Analysis (IPA). Finally, the DGIDB database was used to predict the potential therapeutic drugs to target the identified key genes.
Result:
Based on mRNA, lncRNA and circRNA expression data, we found that differentially expressed mRNAs were enriched in oxygen transport, neutrophil activation, immune response, and oxygen binding. Then the pearson correlation between mRNAs of 46 key genes and lncRNAs and cricRNAs were calculated, and the correlation greater than 0.9 were selected to construct the co-expression network of “mRNA-lncRA” and “mRNA-cricRNA.” Moreover, a “lncRNA-miRNA-mRNA” network and a “circRNA-miRNA-mRNA” network were constructed. IPA analysis showed that the 46 key genes were significantly associated with inflammatory activation and acute respiratory distress syndrome. The constructed TF-mRNA regulatory network was composed of 274 nodes and 573 interacting pairs. 251 potential therapeutic drugs were identified from the DGIDB database.
Conclusion:
This study analyzed the differential genes associated with benign tracheal stenosis and explored the potential regulatory mechanisms, providing a scientific reference for further studies on the pathogenesis of benign tracheal stenosis.