Identification of biomarkers of venous thromboembolism by bioinformatics analyses

Wang, Guiming; Zhao, Wenbo; Yang, Yudong; Yang, Gaochao; Wei, Zhigang; Guo, Jiansheng

doi:10.1097/md.0000000000010152

Cited by 9 publications

(5 citation statements)

References 34 publications

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“…It has been indicated that combination of a microarray technology with a bioinformatics analysis method could comprehensively analyze the expression changes of genes in VTE patients. 6 However, there are no bioinformatics analyses published on the link between differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) in VTE.…”

Section: Introductionmentioning

confidence: 99%

Integrated Bioinformatics Analysis Identifies microRNA-200a-5p as a New Plasma Marker in Patients with Venous Thromboembolism

Lan

Tong

et al. 2022

Annals of Vascular Surgery

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Section: Introductionmentioning

confidence: 99%

Integrated Bioinformatics Analysis Identifies microRNA-200a-5p as a New Plasma Marker in Patients with Venous Thromboembolism

Lan

Tong

et al. 2022

Annals of Vascular Surgery

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“…It has been reported that TP53 is involved in hemostasis and trombosis associated pathway [ 27 ]. TP53 is a potential diagnosis and treatment target for venous thromboembolism [ 28 ]. Our result indicated that down‐regulated hsa‐miR‐150‐5p could play an important role in the coagulation process of deep venous thrombosis via regulating PRKCA, SP1 and TP53.…”

Section: Discussionmentioning

confidence: 99%

Deep sequencing of circulating miRNAs and target mRNAs level in deep venous thrombosis patients

Wang

Chang

Yang

et al. 2023

IET Systems Biology

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Deep venous thrombosis is one of the most common peripheral vascular diseases that lead to major morbidity and mortality. The authors aimed to identify potential differentially expressed miRNAs and target mRNAs, which were helpful in understanding the potential molecule mechanism of deep venous thrombosis. The plasma samples of patients with deep venous thrombosis were obtained for the RNA sequencing. Differentially expressed miRNAs were identified, followed by miRNA‐mRNA target analysis. Enrichment analysis was used to analyze the potential biological function of target mRNAs. GSE19151 and GSE173461 datasets were used for expression validation of mRNAs and miRNAs. 131 target mRNAs of 21 differentially expressed miRNAs were identified. Among which, 8 differentially expressed miRNAs including hsa‐miR‐150‐5p, hsa‐miR‐326, hsa‐miR‐144‐3p, hsa‐miR‐199a‐5p, hsa‐miR‐199b‐5p, hsa‐miR‐125a‐5p, hsa‐let‐7e‐5p and hsa‐miR‐381‐3p and their target mRNAs (PRKCA, SP1, TP53, SLC27A4, PDE1B, EPHB3, IRS1, HIF1A, MTUS1 and ZNF652) were found associated with deep venous thrombosis for the first time. Interestingly, PDE1B and IRS1 had a potential diagnostic value for patients. Additionally, 3 important signaling pathways including p53, PI3K‐Akt and MAPK were identified in the enrichment analysis of target mRNAs (TP53, PRKCA and IRS1). Identified circulating miRNAs and target mRNAs and related signaling pathways may be involved in the process of deep venous thrombosis.

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“…Several DEGs encoding ribosomal proteins were also identified and enriched in module 1. The ribosomal family proteins are upregulated in the plasma of VTE patients 71,72 , and are known to trigger venous thrombus formation in aged mice via p53 activation 73 . Furthermore, ribosomal proteins are also detected in circulating platelets and are associated with VTE 74,75 .…”

Section: Discussionmentioning

confidence: 99%

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

Zheng

et al. 2021

Sci Rep

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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.

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Identification of biomarkers of venous thromboembolism by bioinformatics analyses

Cited by 9 publications

References 34 publications

Integrated Bioinformatics Analysis Identifies microRNA-200a-5p as a New Plasma Marker in Patients with Venous Thromboembolism

Integrated Bioinformatics Analysis Identifies microRNA-200a-5p as a New Plasma Marker in Patients with Venous Thromboembolism

Deep sequencing of circulating miRNAs and target mRNAs level in deep venous thrombosis patients

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

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