Identification and Validation of miRNA-TF-mRNA Regulatory Networks in Uterine Fibroids

Abstract

Uterine fibroids (UF) are the most common benign gynecologic tumors and lead to heavy menstrual bleeding, severe anemia, abdominal pain, and infertility, which seriously harm a women’s health. Unfortunately, the regulatory mechanisms of UF have not been elucidated. Recent studies have demonstrated that miRNAs play a vital role in the development of uterine fibroids. As a high-throughput technology, microarray is utilized to identify differentially expressed genes (DEGs) and miRNAs (DEMs) between UF and myometrium. We identified 373 candidate DEGs and the top 100 DEMs. Function enrichment analysis showed that candidate DEGs were mainly enriched in biological adhesion, locomotion and cell migration, and collagen-containing extracellular matrix. Subsequently, protein-protein interaction (PPI) networks are constructed to analyze the functional interaction between DEGs and screen hub DEGs. Subsequently, the expression levels of hub DEGs were validated by real-time PCR of clinical UF samples. The DGIdb database was used to select candidate drugs for hub DEGs. Molecular docking was applied to test the affinity between proteins and drugs. Furthermore, target genes for 100 candidate DEMs were predicted by miRwalk3.0. After overlapping with 373 candidate DEGs, 28 differentially expressed target genes (DEGTs) were obtained. A miRNA-mRNA network was constructed to investigate the interactions between miRNA and mRNA. Additionally, two miRNAs (hsa-miR-381-3p and hsa-miR-181b-5p) were identified as hub DEMs and validated through RT-PCR. In order to better elucidate the pathogenesis of UF and the synergistic effect between miRNA and transcription factor (TF), we constructed a miRNA-TF-mRNA regulatory network. Meanwhile, in vitro results suggested that dysregulated hub DEMs were associated with the proliferation, migration, and apoptosis of UF cells. Our findings provided a novel horizon to reveal the internal mechanism and novel targets for the diagnosis and treatment of UF.

Identification and comprehensive analysis of circRNA–miRNA–mRNA regulatory networks in osteoarthritis

“…Given the top three ranking of target drugs for hub DEGs, TOP2A, PLK1, and BIRC5, computational molecular docking was applied to identify the best candidates. As shown in previous studies, irinotecan has the strongest binding to BIRC5 through hydrogen bond formation ( 12 ). In this study, digitoxin and oxytetracycline were found to have the greatest binding affinity for TOP2A and PLK1, respectively.…”

“…A PPI network was constructed using the online STRING database ( ) and Cytoscape, as described previously ( 12 ). In addition, hub genes were obtained using molecular complex detection (MCODE) v1.5.1.16 ( 13 ) (degree of cut-off = 2, max.…”

Integrative analysis links autophagy to intrauterine adhesion and establishes autophagy-related circRNA-miRNA-mRNA regulatory network

“…The predicted binding interaction geometries of ML228 towards HIF1A and staurosporine towards PRKCQ were visualized and the docking affinity was scored. PyMol was applied to visualize the optimal drug-protein conformation as previous described [ 22 ].…”