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

Yiming Su,Zhiyong Zheng,Xiaomin Wei,Qiyi Li,Peiyong Hou

doi:10.1038/s41598-021-95909-4

Yiming Su, Zhiyong Zheng + Show 3 more

Open Access

https://doi.org/10.1038/s41598-021-95909-4

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Abstract

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.

Highlights

Venous thromboembolism (VTE) is a complex, multifactorial life-threatening disease that involves vascular endothelial cell (VEC) dysfunction
These results suggest that HIF1α, CBL, ILK and ESM1 play possibly an important role in VTE
We identified several putative unprovoked VTE (uVTE)-associated genes and pathways, along with one transcription factor (TF)-Micro RNAs (miRNAs)-target gene axis, in human Endothelial cells (ECs)

Summary

Introduction

Venous thromboembolism (VTE) is a complex, multifactorial life-threatening disease that involves vascular endothelial cell (VEC) dysfunction. ESM1, HIF1α and the CREB1-miRNA-target genes axis play potential mechanistic roles in uVTE development. MiR-145 is known to reduce thrombogenesis by targeting the coagulation factor XI in vivo[19], and some miRNAs influence the viability of endothelial progenitor cells in DVT patients and enhance thrombus recanalization and r esolution[20]. HIF1α can promote the initiation or development of VTE by enhancing pro-inflammatory and innate immune responses via VEGF and serpin family E member 1 (PAI-1)[24]. These studies indicate that HIF1α plays an important role in maintaining the balance between thrombolysis and thrombosis. A potential role of TFs and the TFmiRNAs axis in the VECs of VTE patients has not been reported so far

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