27 results on '"Just, Annette"'
Search Results
2. Ex vivo modelling of cardiac injury identifies ferroptosis-related pathways as a potential therapeutic avenue for translational medicine
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Abbas, Naisam, Bentele, Marco, Waleczek, Florian J.G., Fuchs, Maximilian, Just, Annette, Pfanne, Angelika, Pich, Andreas, Linke, Sophie, Neumüller, Susanne, Stucki-Koch, Angelika, Jordan, Maria, Perbellini, Filippo, Werlein, Christopher, Korte, Wilhelm, Ius, Fabio, Ruhparwar, Arjang, Weber, Natalie, Fiedler, Jan, and Thum, Thomas
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- 2024
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3. Combined high-throughput library screening and next generation RNA sequencing uncover microRNAs controlling human cardiac fibroblast biology
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Schimmel, Katharina, Stojanović, Stevan D., Huang, Cheng-Kai, Jung, Mira, Meyer, Martin H., Xiao, Ke, Grote-Levi, Lea, Bär, Christian, Pfanne, Angelika, Mitzka, Saskia, Just, Annette, Geffers, Robert, Bock, Katharina, Kenneweg, Franziska, Kleemiß, Felix, Falk, Christine S., Fiedler, Jan, and Thum, Thomas
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- 2021
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4. Pleiotropic cardiac functions controlled by ischemia-induced lncRNA H19
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Hobuß, Lisa, Foinquinos, Ariana, Jung, Mira, Kenneweg, Franziska, Xiao, Ke, Wang, Yong, Zimmer, Karina, Remke, Janet, Just, Annette, Nowak, Juliette, Schmidt, Arne, Pich, Andreas, Mazlan, Stephane, Reamon-Buettner, Stella M., Ramos, Gustavo Campos, Frantz, Stefan, Viereck, Janika, Loyer, Xavier, Boulanger, Chantal, Wollert, Kai C., Fiedler, Jan, and Thum, Thomas
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- 2020
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5. Reconstruction of the miR-506-Quaking axis in Idiopathic Pulmonary Fibrosis using integrative multi-source bioinformatics
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Stojanović, Stevan D., Fuchs, Maximilian, Liang, Chunguang, Schmidt, Kevin, Xiao, Ke, Just, Annette, Pfanne, Angelika, Pich, Andreas, Warnecke, Gregor, Braubach, Peter, Petzold, Christina, Jonigk, Danny, Distler, Jörg H. W., Fiedler, Jan, Thum, Thomas, and Kunz, Meik
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- 2021
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6. Blood-based protein profiling identifies serum protein c-KIT as a novel biomarker for hypertrophic cardiomyopathy
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Sonnenschein, Kristina, Fiedler, Jan, de Gonzalo-Calvo, David, Xiao, Ke, Pfanne, Angelika, Just, Annette, Zwadlo, Carolin, Soltani, Samira, Bavendiek, Udo, Kraft, Theresia, Dos Remedios, Cristobal, Cebotari, Serghei, Bauersachs, Johann, and Thum, Thomas
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- 2021
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7. Long Noncoding RNA-Enriched Vesicles Secreted by Hypoxic Cardiomyocytes Drive Cardiac Fibrosis
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Kenneweg, Franziska, Bang, Claudia, Xiao, Ke, Boulanger, Chantal M., Loyer, Xavier, Mazlan, Stephane, Schroen, Blanche, Hermans-Beijnsberger, Steffie, Foinquinos, Ariana, Hirt, Marc N., Eschenhagen, Thomas, Funcke, Sandra, Stojanovic, Stevan, Genschel, Celina, Schimmel, Katharina, Just, Annette, Pfanne, Angelika, Scherf, Kristian, Dehmel, Susann, Raemon-Buettner, Stella M., Fiedler, Jan, and Thum, Thomas
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- 2019
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8. Inhibition of miR-21: cardioprotective effects in human failing myocardium ex vivo.
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Abbas, Naisam, Haas, Jonas A, Xiao, Ke, Fuchs, Maximilian, Just, Annette, Pich, Andreas, Perbellini, Filippo, Werlein, Christopher, Ius, Fabio, Ruhparwar, Arjang, Fiedler, Jan, Weber, Natalie, and Thum, Thomas
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MICRORNA ,MYOCARDIUM ,NEOVASCULARIZATION ,GENE expression - Abstract
This article, published in the European Heart Journal, explores the effects of inhibiting microRNA-21 (miR-21) on failing human hearts. The study used an ex vivo model of living myocardial slices (LMS) derived from heart failure patients to investigate the direct effects of miR-21 inhibition. The results showed that inhibiting miR-21 led to a suppression of its expression, enhanced cell survival and viability, and improved cardiac function. RNA sequencing analysis revealed significant impacts on cardiac fibrosis, inflammation, and angiogenesis. While the study provides valuable insights, further research is needed to understand the biodistribution and duration of the effects, as well as explore innovative therapeutic approaches for targeted drug delivery. [Extracted from the article]
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- 2024
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9. Identification of miR-143 as a Major Contributor for Human Stenotic Aortic Valve Disease
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Fiedler, Jan, Park, Da-Hee, Hobuß, Lisa, Anaraki, Parnian Kalbasi, Pfanne, Angelika, Just, Annette, Mitzka, Saskia, Dumler, Inna, Weidemann, Frank, Hilfiker, Andres, and Thum, Thomas
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- 2019
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10. Natural Compound Library Screening Identifies New Molecules for the Treatment of Cardiac Fibrosis and Diastolic Dysfunction
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Schimmel, Katharina, Jung, Mira, Foinquinos, Ariana, José, Gorka San, Beaumont, Javier, Bock, Katharina, Grote-Levi, Lea, Xiao, Ke, Bär, Christian, Pfanne, Angelika, Just, Annette, Zimmer, Karina, Ngoy, Soeun, López, Begoña, Ravassa, Susana, Samolovac, Sabine, Janssen-Peters, Heike, Remke, Janet, Scherf, Kristian, Dangwal, Seema, Piccoli, Maria-Teresa, Kleemiss, Felix, Kreutzer, Fabian Philipp, Kenneweg, Franziska, Leonardy, Julia, Hobuß, Lisa, Santer, Laura, Do, Quoc-Tuan, Geffers, Robert, Braesen, Jan Hinrich, Schmitz, Jessica, Brandenberger, Christina, Müller, Dominik N., Wilck, Nicola, Kaever, Volkhard, Bähre, Heike, Batkai, Sandor, Fiedler, Jan, Alexander, Kevin M., Wertheim, Bradley M., Fisch, Sudeshna, Liao, Ronglih, Diez, Javier, González, Arantxa, and Thum, Thomas
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- 2020
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11. Deciphering Pro-angiogenic Transcription Factor Profiles in Hypoxic Human Endothelial Cells by Combined Bioinformatics and in vitro Modeling
- Author
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Schmidt, Arne, Fuchs, Maximilian, Stojanović, Stevan D., Liang, Chunguang, Schmidt, Kevin, Jung, Mira, Xiao, Ke, Weusthoff, Jan, Just, Annette, Pfanne, Angelika, Distler, Jörg H. W., Dandekar, Thomas, Fiedler, Jan, Thum, Thomas, Kunz, Meik, and Publica
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ddc:610 ,Cardiology and Cardiovascular Medicine - Abstract
BackgroundConstant supply of oxygen is crucial for multicellular tissue homeostasis and energy metabolism in cardiac tissue. As a first response to acute hypoxia, endothelial cells (ECs) promote recruitment and adherence of immune cells to the dysbalanced EC barrier by releasing inflammatory mediators and growth factors, whereas chronic hypoxia leads to the activation of a transcription factor (TF) battery, that potently induces expression of growth factors and cytokines including platelet-derived growth factor (PDGF) and vascular endothelial growth factor (VEGF). We report a hypoxia-minded, targeted bioinformatics approach aiming to identify and validate TFs that regulate angiogenic signaling.ResultsA comprehensive RNA-Seq dataset derived from human ECs subjected to normoxic or hypoxic conditions was selected to identify significantly regulated genes based on (i) fold change (normoxia vs. hypoxia) and (ii) relative abundancy. Transcriptional regulation of this gene set was confirmed via qPCR in validation experiments where HUVECs were subjected to hypoxic conditions for 24 h. Screening the promoter and upstream regulatory elements of these genes identified two TFs, KLF5 and SP1, both with a potential binding site within these regions of selected target genes. In vitro, siRNA experiments confirmed SP1- and KLF5-mediated regulation of identified hypoxia-sensitive endothelial genes. Next to angiogenic signaling, we also validated the impact of TFs on inflammatory signaling, both key events in hypoxic sensing. Both TFs impacted on inflammatory signaling since endogenous repression led to increased NF-κB signaling. Additionally, SP1 silencing eventuated decreased angiogenic properties in terms of proliferation and tube formation.ConclusionBy detailed in silico analysis of promoter region and upstream regulatory elements for a list of hypoxia-sensitive genes, our bioinformatics approach identified putative binding sites for TFs of SP or KLF family in vitro. This strategy helped to identify TFs functionally involved in human angiogenic signaling and therefore serves as a base for identifying novel RNA-based drug entities in a therapeutic setting of vascularization.
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- 2022
12. Cardiac fibroblast-derived microRNA passenger strand-enriched exosomes mediate cardiomyocyte hypertrophy
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Bang, Claudia, Batkai, Sandor, Dangwal, Seema, Gupta, Shashi Kumar, Foinquinos, Ariana, Holzmann, Angelika, Just, Annette, Remke, Janet, Zimmer, Karina, Zeug, Andre, Ponimaskin, Evgeni, Schmiedl, Andreas, Yin, Xiaoke, Mayr, Manuel, Halder, Rashi, Fischer, Andre, Engelhardt, Stefan, Wei, Yuanyuan, Schober, Andreas, Fiedler, Jan, and Thum, Thomas
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MicroRNA -- Properties ,Fibroblasts -- Genetic aspects ,Heart enlargement -- Diagnosis ,Health care industry - Abstract
In response to stress, the heart undergoes extensive cardiac remodeling that results in cardiac fibrosis and pathological growth of cardiomyocytes (hypertrophy), which contribute to heart failure. Alterations in microRNA (miRNA) levels are associated with dysfunctional gene expression profiles associated with many cardiovascular disease conditions; however, miRNAs have emerged recently as paracrine signaling mediators. Thus, we investigated a potential paracrine miRNA crosstalk between cardiac fibroblasts and cardiomyocytes and found that cardiac fibroblasts secrete miRNA-enriched exosomes. Surprisingly, evaluation of the miRNA content of cardiac fibroblast-derived exosomes revealed a relatively high abundance of many miRNA passenger strands ('star' miRNAs), which normally undergo intracellular degradation. Using confocal imaging and coculture assays, we identified fibroblast exosomal-derived miR-21_3p ([miR-21.sup.*]) as a potent paracrine-acting RNA molecule that induces cardiomyocyte hypertrophy. Proteome profiling identified sorbin and SH3 domain-containing protein 2 (SORBS2) and PDZ and LIM domain 5 (PDLIM5) as [miR-21.sup.*] targets, and silencing SORBS2 or PDLIM5 in cardiomyocytes induced hypertrophy. Pharmacological inhibition of [miR-21.sup.*] in a mouse model of Ang II-induced cardiac hypertrophy attenuated pathology. These findings demonstrate that cardiac fibroblasts secrete star miRNA-enriched exosomes and identify fibroblast-derived [miR-21.sup.*] as a paracrine signaling mediator of cardiomyocyte hypertrophy that has potential as a therapeutic target., Introduction Cardiac remodeling is a hallmark in the progression of many cardiovascular diseases and is characterized by cardiomyocyte hypertrophy and cardiac fibrosis that lead often to heart failure, a major [...]
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- 2014
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13. MicroRNA-22 increases senescence and activates cardiac fibroblasts in the aging heart
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Jazbutyte, Virginija, Fiedler, Jan, Kneitz, Susanne, Galuppo, Paolo, Just, Annette, Holzmann, Angelika, Bauersachs, Johann, and Thum, Thomas
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- 2013
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14. Integrative Bioinformatic Analyses of Global Transcriptome Data Decipher Novel Molecular Insights into Cardiac Anti-Fibrotic Therapies
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Fuchs, Maximilian, Kreutzer, Fabian Philipp, Kapsner, Lorenz A., Mitzka, Saskia, Just, Annette, Perbellini, Filippo, Terracciano, Cesare M., Xiao, Ke, Geffers, Robert, Bogdan, Christian, Prokosch, Hans-Ulrich, Fiedler, Jan, Thum, Thomas, Kunz, Meik, and HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
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algorithm ,Gene Expression Profiling ,cardiac fibrosis ,integrative bioinformatics ,Computational Biology ,web application ,Fibrosis ,Article ,Workflow ,lcsh:Chemistry ,MicroRNAs ,transcriptomics ,lcsh:Biology (General) ,lcsh:QD1-999 ,big data ,miRNAs ,natural compounds ,Humans ,Gene Regulatory Networks ,ddc:610 ,RNA, Messenger ,Transcriptome ,lcsh:QH301-705.5 - Abstract
Integrative bioinformatics is an emerging field in the big data era, offering a steadily increasing number of algorithms and analysis tools. However, for researchers in experimental life sciences it is often difficult to follow and properly apply the bioinformatical methods in order to unravel the complexity and systemic effects of omics data. Here, we present an integrative bioinformatics pipeline to decipher crucial biological insights from global transcriptome profiling data to validate innovative therapeutics. It is available as a web application for an interactive and simplified analysis without the need for programming skills or deep bioinformatics background. The approach was applied to an ex vivo cardiac model treated with natural anti-fibrotic compounds and we obtained new mechanistic insights into their anti-fibrotic action and molecular interplay with miRNAs in cardiac fibrosis. Several gene pathways associated with proliferation, extracellular matrix processes and wound healing were altered, and we could identify micro (mi) RNA-21-5p and miRNA-223-3p as key molecular components related to the anti-fibrotic treatment. Importantly, our pipeline is not restricted to a specific cell type or disease and can be broadly applied to better understand the unprecedented level of complexity in big data research.
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- 2020
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15. Hypoxic preconditioning of macrophages as therapeutic strategy for ischemic cardiac injury
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Sansonetti, Marida, Waleczek, Florian, Thum, Sabrina, Pfanne, Angelika, Just, Annette, Jung, Mira, and Thum, Thomas
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- 2022
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16. Cardiac endurance training alters plasma profiles of circular RNA MBOAT2.
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Meinecke, Anna, Mitzka, Saskia, Just, Annette, Cushman, Sarah, Stojanović, Stevan D., Ke Xiao, Mooren, Frank C., Fiedler, Jan, and Thum, Thomas
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CIRCULAR RNA ,MARATHON running ,ENDURANCE athletes ,NON-coding RNA ,EXERCISE ,PHYSICAL activity - Abstract
Marathon running is an extreme physical activity, which determines cardiopulmonary adaption of athletes. Circular RNAs (circRNAs) as potential biomarkers in the blood stream have so far not been tested after such strenuous activities. In silico approaches were performed to identify the potential candidate circRNA MBOAT2. Next, we demonstrated high stability and conservation of circRNA MBOAT2 as well as its abundancy in human plasma. In addition to Sanger sequencing of the circRNA specific head-to-tail junction, or back-splice site, we established a synthetic plasmid standard which allowed exact copy number calculations of circRNA MBOAT2. We then analyzed plasmatic circRNA MBOAT2 and observed a significantly lower level 24 h after the marathon. Such alterations were correlated to physical exercise parameters confirming the role of circRNA MBOAT2 as a promising noncoding RNA biomarker detecting cardiopulmonary adaption. [ABSTRACT FROM AUTHOR]
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- 2020
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17. Inflammatory Drivers of Cardiovascular Disease: Molecular Characterization of Senescent Coronary Vascular Smooth Muscle Cells.
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Stojanović, Stevan D., Fuchs, Maximilian, Kunz, Meik, Xiao, Ke, Just, Annette, Pich, Andreas, Bauersachs, Johann, Fiedler, Jan, Sedding, Daniel, and Thum, Thomas
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VASCULAR smooth muscle ,CONTRACTILE proteins ,MUSCLE cells ,CELLULAR aging ,CARDIOVASCULAR diseases ,CORONARY disease ,ATHEROSCLEROSIS - Abstract
The senescence of vascular smooth muscle cells (VSMCs) has been implicated as a causal pro-inflammatory mechanism for cardiovascular disease development and progression of atherosclerosis, the instigator of ischemic heart disease. Contemporary limitations related to studying this cellular population and senescence-related therapeutics are caused by a lack of specific markers enabling their detection. Therefore, we aimed to profile a phenotypical and molecular signature of senescent VSMCs to allow reliable identification. To achieve this goal, we have compared non-senescent and senescent VSMCs from two in vitro models of senescence, replicative senescence (RS) and DNA-damage induced senescence (DS), by analyzing the expressions of established senescence markers: cell cycle inhibitors- p16 INK4a, p14 ARF, p21 and p53; pro-inflammatory factors-Interleukin 1β (IL-1β), IL-6 and high mobility group box-1 (HMGB-1); contractile proteins-smooth muscle heavy chain- (MYH11), smoothelin and transgelin (TAGLN), as well as structural features (nuclear morphology and LMNB1 (Lamin B1) expression). The different senescence-inducing modalities resulted in a lack of the proliferative activity. Nucleomegaly was seen in senescent VSMC as compared to freshly isolated VSMC Phenotypically, senescent VSMC appeared with a significantly larger cell size and polygonal, non-spindle-shaped cell morphology. In line with the supposed switch to a pro-inflammatory phenotype known as the senescence associated secretory phenotype (SASP), we found that both RS and DS upregulated IL-1β and released HMGB-1 from the nucleus, while RS also showed IL-6 upregulation. In regard to cell cycle-regulating molecules, we detected modestly increased p16 levels in both RS and DS, but largely inconsistent p21, p14ARF, and p53 expressions in senescent VSMCs. Since these classical markers of senescence showed insufficient deregulation to warrant senescent VSMC detection, we have conducted a non-biased proteomics and in silico analysis of RS VSMC demonstrating altered RNA biology as the central molecular feature of senescence in this cell type. Therefore, key proteins involved with RNA functionality, HMGB-1 release, LMNB-1 downregulation, in junction with nuclear enlargement, can be used as markers of VSMC senescence, enabling the detection of these pathogenic pro-inflammatory cells in future therapeutic studies in ischemic heart disease and atherosclerosis. [ABSTRACT FROM AUTHOR]
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- 2020
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18. Therapeutic modulation of RNA-binding protein Rbm38 facilitates re-endothelialization after arterial injury.
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Sonnenschein, Kristina, Fiedler, Jan, Pfanne, Angelika, Just, Annette, Mitzka, Saskia, Geffers, Robert, Pich, Andreas, Bauersachs, Johann, and Thum, Thomas
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RNA-binding proteins ,ARTERIAL injuries ,TRANSLUMINAL angioplasty ,PERIPHERAL vascular diseases ,CAROTID artery ,CARRIER proteins ,PROTEIN binding - Abstract
Aims Delayed re-endothelialization after balloon angioplasty in patients with coronary or peripheral artery disease impairs vascular healing and leads to neointimal proliferation. In the present study, we examined the effect of RNA-binding motif protein 38 (Rbm38) during re-endothelialization in a murine model of experimental vascular injury. Methods and results Left common carotid arteries of C57BL/6 mice were electrically denudated and endothelial regeneration was evaluated. Profiling of RNA-binding proteins revealed dysregulated expression of Rbm38 in the denudated and regenerated areas. We next tested the importance of Rbm38 in human umbilical vein endothelial cells (HUVECS) and analysed its effects on cellular proliferation, migration and apoptosis. Rbm38 silencing in vitro demonstrated important beneficial functional effects on migratory capacity and proliferation of endothelial cells. In vivo, local silencing of Rbm38 also improved re-endothelialization of denuded carotid arteries. Luciferase reporter assay identified miR-98 and let-7f to regulate Rbm38 and the positive proliferative properties of Rbm38 silencing in vitro and in vivo were mimicked by therapeutic overexpression of these miRNAs. Conclusion The present data identified Rbm38 as an important factor of the regulation of various endothelial cell functions. Local inhibition of Rbm38 as well as overexpression of the upstream regulators miR-98 and let-7f improved endothelial regeneration in vivo and thus may be a novel therapeutic entry point to avoid endothelial damage after balloon angioplasty. [ABSTRACT FROM AUTHOR]
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- 2019
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19. MicroRNA-Based Therapy of GATA 2-Deficient Vascular Disease.
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Hartmann, Dorothee, Fiedler, Jan, Sonnenschein, Kristina, Just, Annette, Pfanne, Angelika, Zimmer, Karina, Remke, Janet, Foinquinos, Ariana, Butzlaff, Malte, Schimmel, Katharina, Maegdefessel, Lars, Hilfiker-Kleiner, Denise, Lachmann, Nico, Schober, Andreas, Froese, Natali, Heineke, Jörg, Bauersachs, Johann, Batkai, Sandor, and Thum, Thomas
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- 2016
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20. Long noncoding RNA Chast promotes cardiac remodeling.
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Viereck, Janika, Kumarswamy, Regalla, Foinquinos, Ariana, Ke Xiao, Avramopoulos, Petros, Kunz, Meik, Dittrich, Marcus, Maetzig, Tobias, Zimmer, Karina, Remke, Janet, Just, Annette, Fendrich, Jasmin, Scherf, Kristian, Bolesani, Emiliano, Schambach, Axel, Weidemann, Frank, Zweigerdt, Robert, de Windt, Leon J., Engelhardt, Stefan, and Dandekar, Thomas
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VENTRICULAR remodeling ,RNA ,HEART cells ,LABORATORY mice ,CARDIAC hypertrophy - Abstract
The article presents the study on the role of long noncoding (lnc) RNAs in cardiac development. The study reportedly involved an lncRNA microarray analysis in RNA isolated from mouse hearts during sham or transverse aortic constriction. The results revealed that lncRNA cardiac hypertrophy-associated transcript promotes cardiac remodeling.
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- 2016
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21. Functional MicroRNA Library Screening Identifies the HypoxaMiR MiR-24 as a Potent Regulator of Smooth Muscle Cell Proliferation and Vascularization.
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Fiedler, Jan, Stöhr, Andrea, Gupta, Shashi Kumar, Hartmann, Dorothee, Holzmann, Angelika, Just, Annette, Hansen, Arne, Hilfiker-Kleiner, Denise, Eschenhagen, Thomas, and Thum, Thomas
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- 2014
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22. Ratification of NATO enlargement.
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Just, Annette and Goss, Porter J.
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Enlargement of NATO to the former member states of the Warsaw Pact was decided at the July 1997 NATO Summit in Madrid. US President Bill Clinton stated on 30 April 1998 that the addition the three new democracies of the Czech Republic, Hungary, and Poland will ‘strengthen NATO, expand the zone of stability in Europe and reduce the chances American men and women will ever again be called into Europe's fields of battle’. Yet, although the debate in the US Senate over the ratification of the protocols of accession culminated in a favourable decision on 30 April 1998 in favour of the three nations by 80–19, 13 more votes than required for approval, fundamental questions were raised during the process regarding how soon NATO should again enlarge, the costs, and what the future role of the Alliance should be. This article, drafted in October 1997, directly addresses the major arguments launched against the wisdom of a wider NATO. [ABSTRACT FROM PUBLISHER]
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- 1998
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23. Comprehensive Bioinformatics Identifies Key microRNA Players in ATG7-Deficient Lung Fibroblasts.
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Stojanović, Stevan D., Fuchs, Maximilian, Fiedler, Jan, Xiao, Ke, Meinecke, Anna, Just, Annette, Pich, Andreas, Thum, Thomas, and Kunz, Meik
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FIBROBLASTS ,PROTEOMICS ,BIOINFORMATICS ,PULMONARY fibrosis ,LUNGS - Abstract
Background: Deficient autophagy has been recently implicated as a driver of pulmonary fibrosis, yet bioinformatics approaches to study this cellular process are lacking. Autophagy-related 5 and 7 (ATG5/ATG7) are critical elements of macro-autophagy. However, an alternative ATG5/ATG7-independent macro-autophagy pathway was recently discovered, its regulation being unknown. Using a bioinformatics proteome profiling analysis of ATG7-deficient human fibroblasts, we aimed to identify key microRNA (miR) regulators in autophagy. Method: We have generated ATG7-knockout MRC-5 fibroblasts and performed mass spectrometry to generate a large-scale proteomics dataset. We further quantified the interactions between various proteins combining bioinformatics molecular network reconstruction and functional enrichment analysis. The predicted key regulatory miRs were validated via quantitative polymerase chain reaction. Results: The functional enrichment analysis of the 26 deregulated proteins showed decreased cellular trafficking, increased mitophagy and senescence as the major overarching processes in ATG7-deficient lung fibroblasts. The 26 proteins reconstitute a protein interactome of 46 nodes and miR-regulated interactome of 834 nodes. The miR network shows three functional cluster modules around miR-16-5p, miR-17-5p and let-7a-5p related to multiple deregulated proteins. Confirming these results in a biological setting, serially passaged wild-type and autophagy-deficient fibroblasts displayed senescence-dependent expression profiles of miR-16-5p and miR-17-5p. Conclusions: We have developed a bioinformatics proteome profiling approach that successfully identifies biologically relevant miR regulators from a proteomics dataset of the ATG-7-deficient milieu in lung fibroblasts, and thus may be used to elucidate key molecular players in complex fibrotic pathological processes. The approach is not limited to a specific cell-type and disease, thus highlighting its high relevance in proteome and non-coding RNA research. [ABSTRACT FROM AUTHOR]
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- 2020
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24. MicroRNA-Based Therapy of GATA2-Deficient Vascular Disease.
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Hartmann, Dorothee, Fiedler, Jan, Sonnenschein, Kristina, Just, Annette, Pfanne, Angelika, Zimmer, Karina, Remke, Janet, Foinquinos, Ariana, Butzlaff, Malte, Schimmel, Katharina, Maegdefessel, Lars, Hilfiker-Kleiner, Denise, Lachmann, Nico, Schober, Andreas, Froese, Natali, Heineke, Joerg, Bauersachs, Johann, Batkai, Sandor, Thum, Thomas, and Heineke, Jörg
- Published
- 2016
25. Development of Long Noncoding RNA-Based Strategies to Modulate Tissue Vascularization.
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Fiedler, Jan, Breckwoldt, Kaja, Remmele, Christian W., Hartmann, Dorothee, Dittrich, Marcus, Pfanne, Angelika, Just, Annette, Xiao, Ke, Kunz, Meik, Müller, Tobias, Hansen, Arne, Geffers, Robert, Dandekar, Thomas, Eschenhagen, Thomas, and Thum, Thomas
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- *
CELL culture , *CELL physiology , *CELLULAR signal transduction , *EPITHELIAL cells , *GENES , *PROTEINS , *RNA , *TISSUE engineering , *PATHOLOGIC neovascularization , *SEQUENCE analysis - Abstract
Background: Long noncoding ribonucleic acids (lncRNAs) are a subclass of regulatory noncoding ribonucleic acids for which expression and function in human endothelial cells and angiogenic processes is not well studied.Objectives: The authors discovered hypoxia-sensitive human lncRNAs via next-generation ribonucleic acid sequencing and microarray approaches. To address their functional importance in angiogenic processes, several endothelial lncRNAs were characterized for their angiogenic characteristics in vitro and ex vivo.Methods: Ribonucleic acid sequencing and microarray-derived data showed specific endothelial lncRNA expression changes after hypoxia. Validation experiments confirmed strong hypoxia-dependent activation of 2 intergenic lncRNAs: LINC00323 and MIR503HG.Results: Silencing of these lncRNA transcripts led to angiogenic defects, including repression of growth factor signaling and/or the key endothelial transcription factor GATA2. Endothelial loss of these hypoxia-driven lncRNAs impaired cell-cycle control and inhibited capillary formation. The potential clinical importance of these endothelial lncRNAs to vascular structural integrity was demonstrated in an ex vivo model of human induced pluripotent stem cell-based engineered heart tissue.Conclusions: The authors report an expression atlas of human hypoxia-sensitive lncRNAs and identified 2 lncRNAs with important functions to sustain endothelial cell biology. LncRNAs hold great promise to serve as important future therapeutic targets of cardiovascular disease. [ABSTRACT FROM AUTHOR]- Published
- 2015
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26. Deciphering Pro-angiogenic Transcription Factor Profiles in Hypoxic Human Endothelial Cells by Combined Bioinformatics and in vitro Modeling.
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Schmidt A, Fuchs M, Stojanović SD, Liang C, Schmidt K, Jung M, Xiao K, Weusthoff J, Just A, Pfanne A, Distler JHW, Dandekar T, Fiedler J, Thum T, and Kunz M
- Abstract
Background: Constant supply of oxygen is crucial for multicellular tissue homeostasis and energy metabolism in cardiac tissue. As a first response to acute hypoxia, endothelial cells (ECs) promote recruitment and adherence of immune cells to the dysbalanced EC barrier by releasing inflammatory mediators and growth factors, whereas chronic hypoxia leads to the activation of a transcription factor (TF) battery, that potently induces expression of growth factors and cytokines including platelet-derived growth factor (PDGF) and vascular endothelial growth factor (VEGF). We report a hypoxia-minded, targeted bioinformatics approach aiming to identify and validate TFs that regulate angiogenic signaling., Results: A comprehensive RNA-Seq dataset derived from human ECs subjected to normoxic or hypoxic conditions was selected to identify significantly regulated genes based on (i) fold change (normoxia vs. hypoxia) and (ii) relative abundancy. Transcriptional regulation of this gene set was confirmed via qPCR in validation experiments where HUVECs were subjected to hypoxic conditions for 24 h. Screening the promoter and upstream regulatory elements of these genes identified two TFs, KLF5 and SP1, both with a potential binding site within these regions of selected target genes. In vitro , siRNA experiments confirmed SP1- and KLF5-mediated regulation of identified hypoxia-sensitive endothelial genes. Next to angiogenic signaling, we also validated the impact of TFs on inflammatory signaling, both key events in hypoxic sensing. Both TFs impacted on inflammatory signaling since endogenous repression led to increased NF-κB signaling. Additionally, SP1 silencing eventuated decreased angiogenic properties in terms of proliferation and tube formation., Conclusion: By detailed in silico analysis of promoter region and upstream regulatory elements for a list of hypoxia-sensitive genes, our bioinformatics approach identified putative binding sites for TFs of SP or KLF family in vitro . This strategy helped to identify TFs functionally involved in human angiogenic signaling and therefore serves as a base for identifying novel RNA-based drug entities in a therapeutic setting of vascularization., Competing Interests: TT has filed and licensed patents regarding non-coding RNAs in CVD. TT is founder and shareholder of Cardior Pharmaceuticals GmbH. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Schmidt, Fuchs, Stojanović, Liang, Schmidt, Jung, Xiao, Weusthoff, Just, Pfanne, Distler, Dandekar, Fiedler, Thum and Kunz.)
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- 2022
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27. miRNome Profiling of Purified Endoderm and Mesoderm Differentiated from hESCs Reveals Functions of miR-483-3p and miR-1263 for Cell-Fate Decisions.
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Ishikawa D, Diekmann U, Fiedler J, Just A, Thum T, Lenzen S, and Naujok O
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- Cells, Cultured, Endoderm metabolism, Human Embryonic Stem Cells cytology, Humans, Kruppel-Like Factor 4, Kruppel-Like Transcription Factors genetics, Kruppel-Like Transcription Factors metabolism, Mesoderm metabolism, MicroRNAs metabolism, Phosphoglycerate Mutase genetics, Phosphoglycerate Mutase metabolism, Receptor, Platelet-Derived Growth Factor alpha genetics, Receptor, Platelet-Derived Growth Factor alpha metabolism, Cell Differentiation, Endoderm cytology, Human Embryonic Stem Cells metabolism, Mesoderm cytology, MicroRNAs genetics
- Abstract
Pluripotent stem cells hold great promise for regenerative medicine since they can differentiate into all somatic cells. MicroRNAs (miRNAs) could be important for the regulation of these cell-fate decisions. Profiling of miRNAs revealed 19 differentially expressed miRNAs in the endoderm and 29 in the mesoderm when analyzing FACS-purified cells derived from human embryonic stem cells. The mesodermal-enriched miR-483-3p was identified as an important regulator for the generation of mesodermal PDGFRA
+ paraxial cells. Repression of its target PGAM1 significantly increased the number of PDGFRA+ cells. Furthermore, miR-483-3p, miR-199a-3p, and miR-214-3p might also have functions for the mesodermal progenitors. The endoderm-specific miR-489-3p and miR-1263 accelerated and increased endoderm differentiation upon overexpression. KLF4 was identified as a target of miR-1263. RNAi-mediated downregulation of KLF4 partially mimicked miR-1263 overexpression. Thus, the effects of this miRNA were mediated by facilitating differentiation through destabilization of pluripotency along with other not yet defined targets., (Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.)- Published
- 2017
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