Screening Feature Genes of Venous Thromboembolism with DNA Microarray

Integrated bioinformatics analysis identifies microRNA-200a-5p as a new plasma marker in patient with venous thromboembolism

AIMS

Venous thromboembolism (VTE) is a major global health problem with high incidence and mortality. Vein endothelial cell (VEC) dysfunction is the primary cause of VTE. MicroRNAs (miRNAs) assist in the regulation of VEC functional pathways. Our objective was to identify potential miRNA target genes associated with VTE.

MATERIALS AND METHODS

To explore the association between mRNAs and miRNAs in VTE, we performed mRNA or miRNA microarray analysis and experiments in vitro. In addition, five online bioinformatics tools identified the target genes of differentially expressed miRNAs, and miRNA-gene network was constructed. As a result, hub miRNA and mRNA were confirmed. Finally, wound healing assay and transwell migration assay were performed to elucidate the effect of hub miRNA in VEC. Luciferase reporter assay and real-time quantitative polymerase chain reaction (RT-qPCR) were performed to decide the role of miRNA in the expression of hub mRNA.

RESULTS

Screening identified eight overlapping dysregulated genes in patients with VTE, three of which demonstrated significantly decreased expression of miR-200a-5p. Low expression miR-200a-5p in VTE patients is confirmed by ROC analysis (AUC=0.800, P=0.023) and binary logistic regression (OR=0.359, 95% confidence interval: 0.605-0.995). RT-qPCR results showed that miR-200a-5p level was decreased in hypoxia VEC (P=0.038). MiR-200a-5p significantly promoted the migration ability of VEC. The result of Dual-luciferase reporter assay showed that cytochrome coxidaseⅦc(COX7C) directly inhibit the miR-200a-5p expression by binding 5'UTR of miR-200a-5p (P=0.011).

CONCLUSIONS

We anticipate that miR-200a-5p-COX7C pair might be involved in the progression of VTE. Moreover, miR-200a-5p might be a therapeutic target for VTE.

Identification of genes, pathways and transcription factor-miRNA-target gene networks and experimental verification in venous thromboembolism

Venous thromboembolism (VTE) is a complex, multifactorial life-threatening disease that involves vascular endothelial cell (VEC) dysfunction. However, the exact pathogenesis and underlying mechanisms of VTE are not completely clear. The aim of this study was to identify the core genes and pathways in VECs that are involved in the development and progression of unprovoked VTE (uVTE). The microarray dataset GSE118259 was downloaded from the Gene Expression Omnibus database, and 341 up-regulated and 8 down-regulated genes were identified in the VTE patients relative to the healthy controls, including CREB1, HIF1α, CBL, ILK, ESM1 and the ribosomal protein family genes. The protein–protein interaction (PPI) network and the transcription factor (TF)-miRNA-target gene network were constructed with these differentially expressed genes (DEGs), and visualized using Cytoscape software 3.6.1. Eighty-nine miRNAs were predicted as the targeting miRNAs of the DEGs, and 197 TFs were predicted as regulators of these miRNAs. In addition, 237 node genes and 4 modules were identified in the PPI network. The significantly enriched pathways included metabolic, cell adhesion, cell proliferation and cellular response to growth factor stimulus pathways. CREB1 was a differentially expressed TF in the TF-miRNA-target gene network, which regulated six miRNA-target gene pairs. The up-regulation of ESM1, HIF1α and CREB1 was confirmed at the mRNA and protein level in the plasma of uVTE patients. Taken together, ESM1, HIF1α and the CREB1-miRNA-target genes axis play potential mechanistic roles in uVTE development.

Bioinformatics Analysis and Identification of Genes and Molecular Pathways Involved in Venous Thromboembolism (VTE)

OBJECTIVES

To explore the key genes, and correlated pathways in venous thromboembolism (VTE) via bioinformatic analysis, and expected our findings could contribute to the development of new biomarkers and therapeutic target for VTE.

METHODS

Two VTE-related microarray expression profiles (GSE48000 and GSE19151) were downloaded from the Gene Expression Ominibus (GEO) database. Differentially expressed genes (DEGs) were analyzed using limma package, and overlapping DEGs were identified form the above two expression profiles. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEEG) pathway enrichment analyses were performed by DAVID. Protein-protein interaction (PPI) network was constructed by using STRING and visualized with Cytoscape. Furthermore, module analysis plus centrality analysis of the PPI network were executed to identify the potential key genes. Finally, the pathway analysis was performed using GenCLiP 3.0.

RESULTS

A total of 173 DEGs (125 upregulated and 48 downregulated) were identified. GO analysis demonstrated that DEGs were mainly enriched in viral life cycle, ribosome and structural constituent of ribosome. Meanwhile, KEGG pathway analysis showed that these genes were enriched in ribosome, Parkinson's disease and cell cycle. Additionally, one most significant module and 12 hub genes were found. Finally, 6 key genes, namely ISG15, RPS15A, MRPL13, ICT1, MRPL15 and RPLP0, with high centrality features were identified. These key genes were mainly involved in translation, metabolism of proteins and ribosome pathway.

CONCLUSIONS

In summary, these 6 identified genes and correlated pathways should play an important role in VTE, which can provide new insight into the molecular mechanism, potential biomarkers and therapeutic targets associated with VTE.