Transcriptomic Analysis of Long Non-coding RNAs and mRNAs in a Mouse Model of Venous Thrombosis
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE269352 | GEO | 2025/02/19
REPOSITORIES: GEO
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Project description:Deep vein thrombosis (DVT) is a common clinical problem, but its cellular and molecular mechanisms remain incompletely understood. We performed single-cell RNA sequencing (scRNA-seq) on the vein wall of mouse inferior vena cava (IVC) ligation model of deep vein thrombosis (DVT), to analyze the transcriptomic changes in the vein wall during acute venous thrombosis.
2023-02-10 | GSE221978 | GEO
Project description:Venous thromboembolism (VTE) comprising deep venous thrombosis and pulmonary embolism is a main cause of morbidity and mortality that causes tremendous health care costs. Short term immobility related conditions arising from hospitalization, acute trauma and forced bed rest are major risk factors for the development of VTE. In contrast, chronically paralyzed patients with post-spinal cord injury are protected from VTE despite immobilization. Similarly, free-ranging brown bears (Ursus arctos) that hibernate (immobilize) have adapted to this threat through yet to be discovered mechanisms and do not develop VTE. This suggests that long-term immobility can induce antithrombotic mechanisms that are evolutionarily conserved. Here we aimed to identify these adaptive mechanisms of VTE protection in a cross-species approach. Mass spectrometry-based proteomics identified platelet expressed heat shock protein 47 (Hsp47) as the most substantially downregulated protein during brown bear hibernation. In a clinical bed rest study and in spinal-cord injured humans, we likewise observed drastic reduction of platelet-expressed Hsp47. Genetic ablation and pharmaceutical inhibition of platelet Hsp47 attenuates deep vein thrombosis and thromboinflammatory responses in mice and human blood cells. This suggests that Hsp47 downregulation is an evolutionarily conserved mechanism that also protects immobilized patients from VTE. Our translational approach thus identified an antithrombotic signature that may give rise to novel antithrombotic therapeutics and prognostic markers.
2023-04-14 | PXD031521 | Pride
Project description:Venous thromboembolism (VTE) comprising deep venous thrombosis and pulmonary embolism is a main cause of morbidity and mortality that causes tremendous health care costs. Short term immobility related conditions arising from hospitalization, acute trauma and forced bed rest are major risk factors for the development of VTE. In contrast, chronically paralyzed patients with post-spinal cord injury are protected from VTE despite immobilization. Similarly, free-ranging brown bears (Ursus arctos) that hibernate (immobilize) have adapted to this threat through yet to be discovered mechanisms and do not develop VTE. This suggests that long-term immobility can induce antithrombotic mechanisms that are evolutionarily conserved. Here we aimed to identify these adaptive mechanisms of VTE protection in a cross-species approach. Mass spectrometry-based proteomics identified platelet expressed heat shock protein 47 (Hsp47) as the most substantially downregulated protein during brown bear hibernation. In a clinical bed rest study and in spinal-cord injured humans, we likewise observed drastic reduction of platelet-expressed Hsp47. Genetic ablation and pharmaceutical inhibition of platelet Hsp47 attenuates deep vein thrombosis and thromboinflammatory responses in mice and human blood cells. This suggests that Hsp47 downregulation is an evolutionarily conserved mechanism that also protects immobilized patients from VTE. Our translational approach thus identified an antithrombotic signature that may give rise to novel antithrombotic therapeutics and prognostic markers.
2023-04-14 | PXD030465 | Pride
Project description:Venous thromboembolism (VTE) comprising deep venous thrombosis and pulmonary embolism is a main cause of morbidity and mortality that causes tremendous health care costs. Short term immobility related conditions arising from hospitalization, acute trauma and forced bed rest are major risk factors for the development of VTE. In contrast, chronically paralyzed patients with post-spinal cord injury are protected from VTE despite immobilization. Similarly, free-ranging brown bears (Ursus arctos) that hibernate (immobilize) have adapted to this threat through yet to be discovered mechanisms and do not develop VTE. This suggests that long-term immobility can induce antithrombotic mechanisms that are evolutionarily conserved. Here we aimed to identify these adaptive mechanisms of VTE protection in a cross-species approach. Mass spectrometry-based proteomics identified platelet expressed heat shock protein 47 (Hsp47) as the most substantially downregulated protein during brown bear hibernation. In a clinical bed rest study and in spinal-cord injured humans, we likewise observed drastic reduction of platelet-expressed Hsp47. Genetic ablation and pharmaceutical inhibition of platelet Hsp47 attenuates deep vein thrombosis and thromboinflammatory responses in mice and human blood cells. This suggests that Hsp47 downregulation is an evolutionarily conserved mechanism that also protects immobilized patients from VTE. Our translational approach thus identified an antithrombotic signature that may give rise to novel antithrombotic therapeutics and prognostic markers.
2023-04-14 | PXD039087 | Pride
Project description:NHLBI TOPMed: Mayo Clinic Venous Thromboembolism (VTE) Study
| PRJNA393377 | ENA
Project description:NHLBI TOPMed: Mayo Clinic Venous Thromboembolism (VTE) Study
| PRJNA393376 | ENA
Project description:<p><b>Overview:</b><br/> <u>Our overall long-term goal is to determine risk factors for the complex (multifactorial) disease, venous thromboembolism (<b>VTE</b>), that will allow physicians to stratify individual patient risk and target VTE prophylaxis to those who would benefit most.</u> In this genome-wide association case-control study (1300 cases and 1300 controls) we hope to identify susceptibility variants for VTE.</p> <p>Mutations within genes encoding for important components of the anticoagulant, procoagulant, fibrinolytic, and innate immunity pathways are risk factors for VTE. We hypothesize that other genes within these four pathways or within other pathways also are VTE disease-susceptibility genes. Therefore, we performed a genome wide association (GWA) screen and analysis using the Illumina 660W platform to identify SNPs within 1,300 clinic-based, non-cancer VTE cases primarily from Minnesota and the upper Midwest USA, and 1300 clinic-based, unrelated controls frequency-matched on patient age, gender, myocardial infarction/stroke status and state of residence.</p> <p>This is a subset of a slightly larger candidate gene study using 1500 case-control pairs to identify haplotype-tagging SNPs (<b>ht</b>-SNPs) in a large set of candidate genes (n~750) within the anticoagulant, procoagulant, fibrinolytic, and innate immunity pathways.</p> <p><b>Study Populations.</b><br/> <b><u>Cases</u>.</b> VTE cases were consecutive Mayo Clinic outpatients with objectively-diagnosed deep vein thrombosis (DVT) and/or pulmonary embolism (PE) residing in the upper Midwest and referred by Mayo Clinic physician to the Mayo Clinic Special Coagulation Laboratory for clinical diagnostic testing to evaluate for an acquired or inherited thrombophilia, or to the Mayo Clinic Thrombophilia Center. Any person contacted to be a control but discovered to have had a VTE was evaluated for inclusion as a case. Cases were primarily residents from Minnesota, Wisconsin, Iowa, Michigan, Illinois, North or South Dakota, Nebraska, Kansas, Missouri and Indiana. A DVT or PE was categorized as objectively diagnosed when (a) confirmed by venography or pulmonary angiography, or pathology examination of thrombus removed at surgery, or (b) if at least one non-invasive test (compression duplex ultrasonography, lung scan, computed tomography scan, magnetic resonance imaging) was positive. A VTE was defined as: <ol> <li>Proximal leg deep vein thrombosis (DVT), which includes the common iliac, internal iliac, external iliac, common femoral, superficial [now termed "femoral"] femoral, deep femoral [sometimes referred to as "profunda" femoral] and/or popliteal veins. (Note: greater and lesser saphenous veins, or other superficial or perforator veins, were not included as proximal or distal leg DVT).</li> <li>Distal leg DVT (or "isolated calf DVT"), which includes the anterior tibial, posterior tibial and/or peroneal veins. (Note: gastrocnemius, soleal and/or sural [e.g., "deep muscular veins" of the calf] vein thrombosis was not included as distal leg DVT).</li> <li>Arm DVT, which includes the axillary, subclavian and/or innominate (brachiocephalic) veins. (Note: jugular [internal or external], cephalic and brachial vein thrombosis was not included in "arm DVT").</li> <li>Hepatic, portal, splenic, superior or inferior mesenteric, and/or renal vein thrombosis. (Note: ovarian, testicular, peri-prostatic and/or pelvic vein thrombosis was not included).</li> <li>Cerebral vein thrombosis (includes cerebral or dural sinus or vein, saggital sinus or vein, and/or transverse sinus or vein thrombosis).</li> <li>Inferior vena cava (IVC) thrombosis</li> <li>Superior vena cava (SVC) thrombosis</li> <li>Pulmonary embolism</li> </ol> </p> <p>Patients with VTE related to active cancer, antiphospholipid syndrome, inflammatory bowel disease, vasculitis, a rheumatoid or other autoimmune disorder, a vascular anomaly (e.g., Klippel-Trénaunay syndrome, etc.), heparin-induced thrombocytopenia, or a mechanical cause for DVT (e.g., arm DVT or SVC thrombosis related to a central venous catheter or transvenous pacemaker, portal and/or splenic vein thrombosis related to liver cirrhosis, IVC thrombosis related to retroperitoneal fibrosis, etc.), with hemodialysis arteriovenous fistula thrombosis, or with prior liver or bone marrow transplantation were excluded. </p> <p><b><u>Controls</u>.</b> A Mayo Clinic outpatient control group was prospectively recruited for this study. Controls were frequency-matched on the age group (18-29, 30-39, 40-49, 50-59, 60-69, 70-79, and 80+ years), sex, myocardial infarction/stroke status, and state of residence distribution of the cases. We selected clinic-based controls using a controls' database of persons undergoing general medical examinations in the Mayo Clinic Departments of General Internal Medicine or Primary Care Internal Medicine. Additionally persons undergoing evaluation at the Mayo Clinic Sports Medicine Center, and the Department of Family Medicine were screened for inclusion as controls.</p> <p>This study is part of the Gene Environment Association Studies initiative (GENEVA, <a href="http://www.genevastudy.org" target="_blank">http://www.genevastudy.org</a>) funded by the trans-NIH Genes, Environment, and Health Initiative (GEI). The overarching goal is to identify novel genetic factors that contribute to venous thrombosis through large-scale genome-wide association studies of 1,300 clinic-based, VTE cases and 1300 clinic-based, unrelated controls. Genotyping was performed at the Johns Hopkins University Center for Inherited Disease Research (CIDR). Data cleaning and harmonization were done at the GEI-funded GENEVA Coordinating Center at the University of Washington.</p>
| phs000289 | dbGaP
Project description:Background: Patients with high-grade gliomas are at high risk of venous thromboembolism (VTE). MicroRNAs (miRNAs) are small non-coding RNAs with multiple roles in tumor biology, hemostasis and platelet function. We aimed to explore the association between plasma miRNAs and risk of VTE in high-grade glioma. Results: We conducted a nested-case control study within 152 patients with WHO grade IV glioma that had been included in the Vienna Cancer and Thrombosis Study (CATS), a prospective cohort study focused on risk factors for VTE in newly diagnosed or recurrent cancer. At study inclusion a single blood draw was taken, and patients were thereafter followed for a maximum of two years. During that time, 24 patients (16%) developed VTE. Of the other 128 patients, we randomly selected 24 age- and sex-matched controls. After sample quality control, the final group size was 21 VTE-patients and 23 without VTE. Small RNA next-generation sequencing of plasma was performed. We observed that hsa-miR-451a was globally the most abundant miRNA. Notably, 51% of all miRNAs showed a correlation with platelet count. The analysis of miRNAs differentially regulated in VTE patients – with and without platelet adjustment – identified potential VTE biomarker candidates such as has-miR- 221-3p. Conclusion: We here provide one of the largest and deepest peripheral blood miRNA datasets of high-grade glioma patients so far. Further, we confirm previous observations of a considerable impact of platelet count on the blood miRNome. And, finally, we present first VTE biomarker candidates that can serve as the starting point for future confirmatory research.
2023-12-31 | GSE222666 | GEO
Project description:Samples were collected from 'control participants' of the Heart and Vascular Health (HVH) study that constitutes a group of population based case control studies of myocardial infarction (MI), stroke, venous thromboembolism (VTE), and atrial fibrillation (AF) conducted among 30-79 year old members of Group Health, a large integrated health care organization in Washington State.
2013-06-08 | GSE47727 | GEO
Project description:Samples were collected from 'control participants' of the Heart and Vascular Health (HVH) study that constitutes a group of population based case control studies of myocardial infarction (MI), stroke, venous thromboembolism (VTE), and atrial fibrillation (AF) conducted among 30-79 year old members of Group Health, a large integrated health care organization in Washington State.
2013-06-08 | GSE47728 | GEO