Circulating microRNA expression and their target genes in deep vein thrombosis: A systematic review and bioinformatics analysis

LncRNA NEAT1 Promotes Vascular Endothelial Cell Dysfunction via miR-218-5p/GAB2 and Serves as a Diagnostic Biomarker for Deep Vein Thrombosis

OBJECTIVE

Deep vein thrombosis (DVT) is a common peripheral disease. This study aimed to elucidate the diagnostic biomarker of lncRNA nuclear-enriched abundant transcript 1 (NEAT1) in the DVT, and explore possible mechanisms in Human umbilical vein endothelial cells (HUVECs).

METHODS

101 patients with lower extremity DVT and 82 healthy controls were enrolled. RT-qPCR was designed to resolve the mRNA levels of NEAT1, miR-218-5p, and GAB2. ROC was applied for the diagnosis of DVT. Systemic inflammation (IL-1β, IL-6, and TNF-α) and adhesion factor (SELP, VCAM-1, and ICAM-1) were examined by the ELISA. And cell proliferation, migration, and apoptosis were conducted by the CCK-8, Transwell, flow cytometry assay. The targeting relationship was validated by Dual luciferase reporter and RIP analysis.

RESULTS

NEAT1 and GAB2 were upregulated in patients with DVT, while miR-218-5p was decreased (P < .01). Serum NEAT1 can identify DVT patients from healthy individuals. NEAT1 was positively correalted with fibrinolysis factors, coagulation factors, and vasoconstrictors. NEAT1 inhibited the proliferation, migration, and promoted apoptosis as well as inflammation and adhesion factors secretion of HUVECs (P < .05), but all were impaired by overexpression of miR-218-5p (P < .05). NEAT1 promoted GAB2 expression in DVT by acting as a sponge for miR-218-5p.

CONCLUSION

Elevated NEAT1 is a possible DVT diagnostic biomarker, and is implicated in vascular endothelial cell dysfunction via miR-218-5p/GAB2 axis.

miR-513c-5p Suppression Aggravates Pyroptosis of Endothelial Cell in Deep Venous Thrombosis by Promoting Caspase-1

Deep vein thrombosis (DVT) is a common peripheral vascular disease. Secondary pulmonary embolism (PE) caused by DVT leads to substantial patient death. Inflammation has been suggested as a key factor in the pathophysiology of DVT, however, involvement of pyroptosis-related inflammatory factors in DVT formation remains unclear. Here, we proposed that post-transcriptional modification of caspase-1 might be a crucial trigger for enhanced pyroptosis in vascular endothelial cells (VECs), and consequently contributed to severer symptoms in DVT patients. In order to explore the involvement of pyroptosis in DVT, peripheral blood mononuclear cells were collected from 30 DVT patients, and compared with the healthy controls, we found caspase-1 was increased both in mRNA and protein levels. miRNA microarray analysis demonstrated that down-regulated miR-513c-5p was significantly negatively correlated with the expression of caspase-1. In vitro assays suggested that miR-513c-5p overexpression could ameliorate the expression of caspase-1, and thus decreased the production of cleaved gasdermin D (GSDMD) and interleukin (IL)-1β and IL-18 in VECs. The dual-luciferase reporter assay identified direct binding between miR-513c-5p and the 3′ untranslated region of caspase-1 encoding gene. The administration of miR-513c-5p mimics through tail vein injection or caspase-1 inhibitor (vx-765) by intraperitoneal injection remarkably decreased the volume of blood clots in vivo, whereas miR-513c-5p inhibitor aggravated thrombosis formation and this effect was dramatically weakened when treated in combination with vx-765. Collectively, these results revealed that the pyroptosis of VECs induced by decreased miR-513c-5p was involved in DVT progression and indicated a potential therapeutic strategy of targeting the miR-513c-5p/caspase-1/GSDMD signal axis for DVT management.

Role and Mechanism of mir-5189-3p in Deep Vein Thrombosis of Lower Extremities

BACKGROUND

This study is to investigate the role and mechanism of mir-5189-3p in deep vein thrombosis (DVT) in lower extremity.

METHODS

The blood samples were collected from Kazakh patients with DVT in lower extremity and were subjected to microRNA sequencing. Bioinformatics were used to identify mir-5189-3p and its target genes. Dual luciferase reporter assay was used to determine the regulatory effect of mir-5189-3p on JAG1. SD rats were randomly divided into normal control, DVT model, hsa-miR-5189-3p mimics and hsa-miR-5189-3p negative control groups. HE staining was used to observe the pathological changes. TUNEL method was used to observe apoptosis. Western blot was used to detect Bax and Bcl-2 protein expression. Real-time quantitative PCR was used to detect JAG1, Notch1 and Hes1 mRNA.

RESULTS

The target of Has-miR-5189-3p was JAG1. Co-transfection of miR-5189-3p mimics and pmirGLO/JAG1 wild-type plasmid induced significantly decreased luciferase activity. In hsa-miR-5189-3p mimics and hsa-miR-5189-3p negative control groups, there were more nucleated cells in the thrombus tissues, and the organization degree obviously increased. Signs of blood flow recanalization were observed. The apoptosis of hsa-miR-5189-3p mimics and hsa-miR-5189-3p negative control groups was lower than that in DVT model group. Furthermore, mir-5189-3p mimics significantly increased the mRNA levels of JAG1, Notch1 and Hes1. Additionally, mir-5189-3p mimics significantly increased Bcl-2 while decreased Bax protein.

CONCLUSIONS

mir-5189-3p could inhibit apoptosis and promote thrombus organization in DVT possibly via Notch signaling pathway. Mir-5189-3p can be used as a potential target for DVT treatment.

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.

MiR-296-5p ameliorates deep venous thrombosis by inactivating S100A4

Deep venous thrombosis is one of the most common venous thromboembolic diseases and has a low cure rate and a high postoperative recurrence rate. Furthermore, emerging evidence indicates that microRNAs are involved in deep venous thrombosis. miR-296-5p is an important microRNA that plays a critical role in various cellular functions, and S100A4 is closely related to vascular function. miR-296-5p is downregulated in deep venous thrombosis patients, and its predicted target S100A4 is upregulated in deep venous thrombosis patients. Therefore, it was hypothesized that miR-296-5p may play a vital role in the development of deep venous thrombosis by targeting S100A4. An Ox-LDL-stimulated HUVEC and deep venous thrombosis mouse model was employed to detect the biological functions of miR-296-5p and S100A4. Dual luciferase reporter assays and pull-down assays were used to authenticate the interaction between miR-296-5p and S100A4. ELISA and Western blotting were employed to detect the protein levels of thrombosis-related factors and the endothelial-to-mesenchymal transition (EndMT)-related factors. The miR-296-5p levels were reduced, while the S100A4 levels were enhanced in deep venous thrombosis patients, and the miR-296-5p levels were negatively correlated with the S100A4 levels in deep venous thrombosis patients. miR-296-5p suppressed S100A4 expression by targeting the 3' UTR of S100A4. MiR-296-5p knockdown accelerated ox-LDL-induced HUVEC apoptosis, oxidative stress, thrombosis-related factor expression, and EndMT, while S100A4 knockdown antagonized these effects in ox-LDL-induced HUVECs. S100A4 knockdown reversed the effect induced by miR-296-5p knockdown. Moreover, the in vivo studies revealed that miR-296-5p knockdown in deep venous thrombosis mice exacerbated deep venous thrombosis formation, whereas S100A4 knockdown had the opposite effect. These results indicate that elevated miR-296-5p inhibits deep venous thrombosis formation by inhibiting S100A4 expression. Both miR-296-5p and S100A4 may be potential diagnostic markers and therapeutic targets for deep venous thrombosis.

A Translational Model for Venous Thromboembolism: MicroRNA Expression in Hibernating Black Bears

BACKGROUND

Hibernating American black bears have significantly different clotting parameters than their summer active counterparts, affording them protection against venous thromboembolism during prolonged periods of immobility. We sought to evaluate if significant differences exist between the expression of microRNAs in the plasma of hibernating black bears compared with their summer active counterparts, potentially contributing to differences in hemostasis during hibernation.

MATERIALS AND METHODS

MicroRNA sequencing was assessed in plasma from 21 American black bears in summer active (n = 11) and hibernating states (n = 10), and microRNA signatures during hibernating and active state were established using both bear and human genome. MicroRNA targets were predicted using messenger RNA (mRNA) transcripts from black bear kidney cells. In vitro studies were performed to confirm the relationship between identified microRNAs and mRNA expression, using artificial microRNA and human liver cells.

RESULTS

Using the bear genome, we identified 15 microRNAs differentially expressed in the plasma of hibernating black bears. Of these microRNAs, three were significantly downregulated (miR-141-3p, miR-200a-3p, and miR-200c-3p), were predicted to target SERPINC1, the gene for antithrombin, and demonstrated regulatory control of the gene mRNA expression in cell studies.

CONCLUSIONS

Our findings suggest that the hibernating black bears' ability to maintain hemostasis and achieve protection from venous thromboembolism during prolonged periods of immobility may be due to changes in microRNA signatures and possible upregulation of antithrombin expression.

Downregulation of interleukin-6 and C-reactive protein underlies a novel inhibitory role of microRNA-136-5p in acute lower extremity deep vein thrombosis

Deep vein thrombosis (DVT) comprises a critical and common health condition with high incidence, mortality, and long-term adverse sequelae. Several differentially expressed microRNAs (miRNAs) have emerged as promising prognostic markers in DVT. The present study intended to explore the functional relevance of miR-136-5p in acute lower extremity DVT (LEDVT). Rat models of acute LEDVT were established and miR-136-5p expression was altered by agomir or antagomir to assess its effects. In addition, in vitro gain- and loss-experiments, prior to exposure to CoCl₂, were performed to investigate effects of miR-136-5p on human umbilical vein endothelial cell (HUVEC) apoptosis and levels of interleukin-6 (IL-6) and C-reactive protein (CRP). miR-136-5p was downregulated, whereas IL-6 and CRP were elevated in acute LEDVT patients. Notably, miR-136-5p was confirmed to target both IL-6 and CRP. Overexpression of miR-136-5p led to reduced length, weight, and ratio of weight to length of the venous thrombus. Furthermore, overexpressed miR-136-5p downregulated the expression of IL-6 and CRP, consequently inhibiting HUVEC apoptosis. Conjointly, our data indicate that the overexpression of miR-136-5p has the potential to bind to the 3’-UTR in the mRNAs for IL-6 and CRP and mitigate acute LEDVT, which provides a basis for new therapeutic targets in acute LEDVT treatment.

Exosomal miR-1246 and miR-155 as predictive and prognostic biomarkers for trastuzumab-based therapy resistance in HER2-positive breast cancer

PURPOSE

This study aimed to investigate the predictive and prognostic roles of circulating exosomal miRNAs in breast cancer treated with trastuzumab-based chemotherapy.

METHODS

Circulating exosomal miRNAs from trastuzumab-resistant (n = 4) and -sensitive (n = 4) patients were profiled using miRNA microarray. The predictive and prognostic roles of filtered miRNAs were validated in 107 early-stage and 68 metastatic patients treated with trastuzumab-based chemotherapy through receiver-operating characteristic (ROC) curve analysis, logistic regression and Cox proportional hazards regression analysis, and Kaplan-Meier survival analysis.

RESULTS

MiRNA microarray analysis revealed miR-1246 and miR-155 were the most up-regulated miRs in trastuzumab-resistant HER2-positive breast cancer patients, which were further validated in trastuzumab-resistant patient samples (n = 32) compared with trastuzumab sensitive ones (n = 36). MiR-1246 showed a ROC curve area of 0.750 with 78.1% sensitivity and 75% specificity in discriminating resistant from sensitive patients (p < 0.001), while miR-155 showed a ROC curve area of 0.877 with 68.8% sensitivity and 97.2% specificity (p < 0.001). Predictive factors and multivariate analysis showed that high levels of miR-1246 and miR-155 strongly predicted poor event-free survival (EFS) for early-stage patients, and poor progression-free survival (PFS) for metastatic patients. However, both miRNAs were revealed not to be associated with overall survival (OS). In addition, Kaplan-Meier survival analysis demonstrated that early-stage and metastatic patients with high expression of miR-1246 and miR-155 had poorer EFS or PFS, respectively, than those with decreased expression of both miRs.

CONCLUSIONS

This study demonstrated the valuable roles of circulating exosomal miR-1246 and miR-155 in distinguishing trastuzumab resistant from sensitive patients.

Circulating microRNA trafficking and regulation: computational principles and practice

Rapid advances in genomics discovery tools and a growing realization of microRNA's implication in intercellular communication have led to a proliferation of studies of circulating microRNA sorting and regulation across cells and different species. Although sometimes, reaching controversial scientific discoveries and conclusions, these studies have yielded new insights in the functional roles of circulating microRNA and a plethora of analytical methods and tools. Here, we consider this body of work in light of key computational principles underpinning discovery of circulating microRNAs in terms of their sorting and targeting, with the goal of providing practical guidance for applications that is focused on the design and analysis of circulating microRNAs and their context-dependent regulation. We survey a broad range of informatics methods and tools that are available to the researcher, discuss their key features, applications and various unsolved problems and close this review with prospects and broader implication of this field.

Role of microRNAs in Hemophilia and Thrombosis in Humans

MicroRNAs (miRNA) play an important role in gene expression at the posttranscriptional level by targeting the untranslated regions of messenger RNA (mRNAs). These small RNAs have been shown to control cellular physiological processes including cell differentiation and proliferation. Dysregulation of miRNAs have been associated with numerous diseases. In the past few years miRNAs have emerged as potential biopharmaceuticals and the first miRNA-based therapies have entered clinical trials. Our recent studies suggest that miRNAs may also play an important role in the pathology of genetic diseases that are currently considered to be solely due to mutations in the coding sequence. For instance, among hemophilia A patients there exist a small subset, with normal wildtype genes; i.e., lacking in mutations in the coding and non-coding regions of the F8 gene. Similarly, in many patients with missense mutations in the F8 gene, the genetic defect does not fully explain the severity of the disease. Dysregulation of miRNAs that target mRNAs encoding coagulation factors have been shown to disturb gene expression. Alterations in protein levels involved in the coagulation cascade mediated by miRNAs could lead to bleeding disorders or thrombosis. This review summarizes current knowledge on the role of miRNAs in hemophilia and thrombosis. Recognizing and understanding the functions of miRNAs by identifying their targets is important in identifying their roles in health and diseases. Successful basic research may result in the development and improvement of tools for diagnosis, risk evaluation or even new treatment strategies.

Transcriptome analysis of Klf15‑mediated inhibitory functions in a mouse deep venous thrombosis model

Krüppel-like family (KLF) members are important regulators of proinflammatory activation in the vasculature. A transcriptome study involving RNA sequencing (RNA-seq) and quantitative PCR (qPCR) was performed to investigate Klf15 and Klf15-regulated gene levels in C57BL/6 mice with inferior vena cava thrombi and in control (Blank) mice. A total of 2,206 differentially expressed genes (DEGs), including 1,330 upregulated and 876 downregulated genes, were identified between the deep venous thrombosis (DVT) group and the Blank group. Additionally, 1,041 DEGs (235 upregulated and 806 downregulated) were identified between the Klf15-small interfering RNA (siRNA) and Klf15-negative control (NC) groups. The DEGs were subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses, and qPCR was conducted to validate the results. A total of seven significant DEGs were selected from the RNA-seq results. Matrix metalloproteinases (Mmp)12, Mmp13, Mmp19, Arg1, Ccl2, heme oxygenase-1 and Fmo3 levels were significantly higher, while Klf15 levels were lower, in the DVT group than in the Blank group. Fmo3 and Mmp19 have not been previously identified as DVT-associated DEGs. Klf15, Mmp12 and Mmp13 levels were compared between the Klf15-siRNA and Klf15-NC groups. Mmp12 and Mmp13 expression was significantly higher, while that of Klf15 was lower, in the Klf15-siRNA group than in the Klf15-NC group. Critical roles of Klf15, Mmp12 and Mmp13 have been identified, which have not previously been shown to help regulate DVT initiation and progression. Moreover, Klf15-mediated regulation of DVT may be modulated by downregulation of various genes, such as Mmp12 and Mmp13, potentially providing a theoretical foundation and diagnostic criteria for DVT treatment.

IL (Interleukin)-6 Contributes to Deep Vein Thrombosis and Is Negatively Regulated by miR-338-5p

Supplemental Digital Content is available in the text.

Objective:

Deep venous thrombosis (DVT), one of the most common venous thromboembolic disorders, is closely linked with pulmonary embolism and post-thrombotic syndrome, both of which have a high mortality. However, the factors that trigger DVT formation are still largely unknown. Elevated expression of IL (interleukin)-6—an important inflammatory cytokine—has been linked with DVT formation. However, the molecular mechanisms leading to the elevated IL-6 in DVT remain unclear. Here, we proposed that epigenetic modification of IL-6 at the post-transcriptional level may be a crucial trigger for IL-6 upregulation in DVT.

Approach and Results:

To explore the association between microRNAs and IL-6 in DVT, we performed microRNA microarray analysis and experiments both in vitro and in vivo. Microarray and quantitative real-time polymerase chain reaction results showed that IL-6 expression was increased while miR-338-5p level was decreased substantially in peripheral blood mononuclear cells of patients with DVT, and there was significant negative correlation between miR-338-5p and IL-6. Experiments in vitro showed that overexpressed miR-338-5p reduced IL-6 expression, while miR-338-5p knockdown increased IL-6 expression. Moreover, our in vivo study found that mice with anti–IL-6 antibody or agomiR-338-5p delivery resulted in decreased IL-6 expression and alleviated DVT formation, whereas antagomiR-338-5p acted inversely. Most of miR-338-5p was found located in cytoplasm by fluorescence in situ hybridization. Dual-luciferase reporter assay identified direct binding between miR-338-5p and IL-6.

Conclusions:

Our results suggest that decreased miR-338-5p promotes DVT formation by increasing IL-6 expression.

Overexpressed microRNA-103a-3p inhibits acute lower-extremity deep venous thrombosis via inhibition of CXCL12

Studies have shown that microRNAs (miRNAs) participate in almost all pathological and physiological processes including acute lower-extremity deep venous thrombosis (LEDVT). Here, this study was designed to elucidate the possible function of miR-103a-3p in acute LEDVT. Expression of miR-103a-3p and chemokine C-X-C motif ligand 12 (CXCL12) was initially quantified in plasma collected from 81 LEDVT patients. Then LEDVT mouse models were established by injection with 3% sodium pentobarbital. The interaction between miR-103a-3p and CXCL12 was identified by dual-luciferase reporter gene assay. After gain- and loss-of-function studies, interleukin-6 (IL-6) and IL-8 and tissue factor (TF) levels, and expression of plasminogen activator inhibitors (PAIs), von Willebrand factor (vWF), thromboxane A2 (TH-A2), F4/80, IL-12, Arginase-1 (Arg-1) and CD206 were determined using enzyme-linked immunosorbent assay (ELISA), reverse transcription quantitative polymerase chain reaction (RT-qPCR) and western blot analysis, respectively. miR-103a-3p was downregulated, while CXCL12 was upregulated in patients and mice with LEDVT. miR-103a-3p targets CXCL12 and inhibited its expression. Overexpressed miR-103a-3p or downregulated CXCL12 decreased expression of IL-6, IL-8, TF, PAIs, vWF, TH-A2, M1 markers (IL-6 and IL-12), yet increased expression of M2 markers (Arg-1 and CD206) in LEDVT mice. Additionally, upregulated miR-103a-3p or silencing CXCL12 suppressed thrombosis in LEDVT mice. However, overexpression of CXCL12 reversed the tendency mentioned above. Altogether, miR-103a-3p can potentially downregulate CXCL12 expression to disrupt inflammatory response and thrombosis, ultimately preventing the development of LEDVT. Our findings underscore a possible alternative therapeutic strategy to limit LEDVT.

The predictive value of circulating microRNAs for venous thromboembolism diagnosis: A systematic review and diagnostic meta-analysis

OBJECTIVE

Venous thromboembolism (VTE) is a common cardiovascular disease, in which pulmonary embolism (PE) is potentially life-threatening. Accurate biological markers for the early diagnosis of VTE are needed. The purpose of this study was to analyze and validate the predictive value of microRNAs for the diagnosis of VTE.

METHODS

A comprehensive literature review was conducted using the PubMed, Embase, and Cochrane Library databases and is current through Sep 27, 2018. The diagnostic value of microRNAs for VTE was analyzed by creating a summary receiver operating characteristic curve (SROC) and calculating the area under the curve (AUC).

RESULTS

Our analysis included 12 articles assessing a total of 1057 individuals. The most frequently researched microRNA was miR-134, and the pooled results of the predictive ability of this miRNA with 95% confidence intervals (CIs) showed an average sensitivity of 0.82 (0.69-0.91) and an average specificity of 0.83 (0.68-0.92). The average AUC for the SROC curves was 0.89 (0.86-0.92). For other microRNAs, AUC values >0.8 were considered as potential diagnostic indices. These microRNAs included miR-1233, miR-134, miR-145, miR-483-3p, miR-582, miR-532, and miR-195.

CONCLUSIONS

MicroRNAs may act as novel diagnostic biomarkers for VTE, and miR-1233, miR-134, miR-145, miR-483-3p, miR-582, miR-532, and miR-195 are prime candidates. Of these, research on miR-134 is the most extensive and reliable.

Semiautomatic intermittent pneumatic compression device applied to deep vein thrombosis in major orthopedic surgery

Objective

To investigate the effect of additional semiautomatic intermittent pneumatic compression device (IPCD) in the prevention of deep vein thrombosis (DVT) of lower extremity in these patients undergoing major orthopedic surgery, when compared with the conventional graduated compression stockings alone.

Methods

The data of 112 patients undergoing major orthopedic surgery were retrospectively analyzed. 51 patients who ever received IPCD and graduated compression stockings during major orthopedic surgery were taken as the experimental group, and 61 patients who only received the conventional graduated compression stockings during surgery were taken as the observation group. The Doppler sonography was utilized to detect the presence of DVT and pulmonary embolism pre- and postoperatively. Besides, the mean and peak velocity of blood flow in femoral vein were recorded before and after surgery. And then, the comparisons between the two groups were made, respectively.

Results

When compared with the conventional graduated compression stockings alone, the intraoperative application of IPCD and stockings contributed the significant reduction of DVT (3.92%, 2/51 versus 9.84%, 6/61, X² = 5.632, P = 0.034). In terms of the mean and peak velocity of blood flow in femoral vein, the postoperative difference was higher in the observation group than those in the control group (149.56 ± 26.35 versus 130.15 ± 22.56 mm/s, P < 0.05). With respect to perioperative blood loss, the difference between the two groups was statistically significant (800.5 ± 320.7 versus 950.1 ± 305.9 ml, P = 0.031).

Conclusions

Intraoperative application of IPCD could promote blood circulation of lower limbs, and significantly decrease the incidence of potentially fatal DVT in patients undergoing major orthopedic surgery, when compared with the conventional graduated compression stockings.