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Berlin Brandenburg

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  • 1
    Description: Program collection the data analysis of the study "Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions" by Westermann et al.,  Nature, 2016...
    Keywords: Dual Rna-Seq
    Source: DataCite
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  • 2
    Language: English
    In: Nature, 28 January 2016, Vol.529(7587), pp.496-501
    Description: Bacteria express many small RNAs for which the regulatory roles in pathogenesis have remained poorly understood due to a paucity of robust phenotypes in standard virulence assays. Here we use a generic 'dual RNA-seq' approach to profile RNA expression simultaneously in pathogen and host during Salmonella enterica serovar Typhimurium infection and reveal the molecular impact of bacterial riboregulators. We identify a PhoP-activated small RNA, PinT, which upon bacterial internalization temporally controls the expression of both invasion-associated effectors and virulence genes required for intracellular survival. This riboregulatory activity causes pervasive changes in coding and noncoding transcripts of the host. Interspecies correlation analysis links PinT to host cell JAK-STAT signalling, and we identify infection-specific alterations in multiple long noncoding RNAs. Our study provides a paradigm for a sensitive RNA-based analysis of intracellular bacterial pathogens and their hosts without physical separation, as well as a new discovery route for hidden functions of pathogen genes.
    Keywords: Gene Expression Regulation -- Genetics ; Host-Pathogen Interactions -- Genetics ; RNA, Bacterial -- Genetics ; RNA, Untranslated -- Genetics ; Salmonella Typhimurium -- Genetics
    ISSN: 00280836
    E-ISSN: 1476-4687
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  • 3
    Language: English
    In: Nucleic acids research, 07 January 2013, Vol.41(1), pp.542-53
    Description: Many microRNAs (miRNAs) are co-regulated during the same physiological process but the underlying cellular logic is often little understood. The conserved, immunomodulatory miRNAs miR-146 and miR-155, for instance, are co-induced in many cell types in response to microbial lipopolysaccharide (LPS) to feedback-repress LPS signalling through Toll-like receptor TLR4. Here, we report that these seemingly co-induced regulatory RNAs dramatically differ in their induction behaviour under various stimuli strengths and act non-redundantly through functional specialization; although miR-146 expression saturates at sub-inflammatory doses of LPS that do not trigger the messengers of inflammation markers, miR-155 remains tightly associated with the pro-inflammatory transcriptional programmes. Consequently, we found that both miRNAs control distinct mRNA target profiles; although miR-146 targets the messengers of LPS signal transduction components and thus downregulates cellular LPS sensitivity, miR-155 targets the mRNAs of genes pervasively involved in pro-inflammatory transcriptional programmes. Thus, miR-155 acts as a broad limiter of pro-inflammatory gene expression once the miR-146 dependent barrier to LPS triggered inflammation has been breached. Importantly, we also report alternative miR-155 activation by the sensing of bacterial peptidoglycan through cytoplasmic NOD-like receptor, NOD2. We predict that dose-dependent responses to environmental stimuli may involve functional specialization of seemingly co-induced miRNAs in other cellular circuitries as well.
    Keywords: Immunity, Innate -- Genetics ; Micrornas -- Metabolism
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 4
    Language: English
    In: Angewandte Chemie International Edition, 03 September 2018, Vol.57(36), pp.11564-11568
    Description: Transgene expression of green fluorescent protein (GFP) has facilitated the spatiotemporal investigation of host–pathogen interactions; however, introduction of the GFP gene remains challenging in drug‐resistant bacteria. Herein, we report a novel far‐red fluorescent nucleic acid stain, , which efficiently labels bacteria through a DNA binding mode without affecting growth and viability. Exemplarily, we stained , a major threat to hospitalized patients, and deciphered divergent interaction strategies of antibiotic‐resistant and antibiotic‐sensitive strains with immune cells. constitutes an off‐the‐shelf reagent for real‐time analysis of bacterial infection, including strains for which the use of genetically encoded reporters is not feasible. Eventually, our approach may aid the development of strategies to combat a major worldwide health threat: multidrug‐resistant bacteria. : The fluorescent labeling agent was developed for real‐time analysis of bacterial infection. This far‐red fluorescent nucleic acid stain efficiently labeled bacteria through DNA binding without affecting their growth or viability. Staining of , a major threat to hospitalized patients, uncovered different interaction strategies of antibiotic‐resistant and antibiotic‐sensitive strains with immune cells.
    Keywords: Antibiotics ; Dna Recognition ; Fluorescence-Activated Cell Sorting ; Far-Red Cyanine Dyes ; Multidrug-Resistant Bacteria
    ISSN: 1433-7851
    E-ISSN: 1521-3773
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  • 5
    Language: English
    In: PLoS ONE, 01 January 2018, Vol.13(2), p.e0193066
    Description: CRISPR/Cas9-based approaches have greatly facilitated targeted genomic deletions. Contrary to coding genes however, which can be functionally knocked out by frame-shift mutagenesis, non-coding RNA (ncRNA) gene knockouts have remained challenging. Here we present a universal ncRNA knockout approach guided by epigenetic hallmarks, which enables robust gene silencing even in provisionally annotated gene loci. We build on previous work reporting the presence of overlapping histone H3 lysine 4 tri-methylation (H3K4me3) and DNaseI hypersensitivity sites around the transcriptional start sites of most genes. We demonstrate that excision of this gene-proximal signature leads to loss of microRNA and lincRNA transcription and reveals ncRNA phenotypes. Exemplarily we demonstrate silencing of the constitutively transcribed MALAT1 lincRNA gene as well as of the inducible miR-146a and miR-155 genes in human monocytes. Our results validate a role of miR-146a and miR-155 in negative feedback control of the activity of inflammation master-regulator NFκB and suggest that cell-cycle control is a unique feature of miR-155. We suggest that our epigenetically guided CRISPR approach may improve existing ncRNA knockout strategies and contribute to the development of high-confidence ncRNA phenotyping applications.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 6
    In: EMBO Journal, 18 May 2011, Vol.30(10), pp.1977-1989
    Description: MicroRNAs have well‐established roles in eukaryotic host responses to viruses and extracellular bacterial pathogens. In contrast, microRNA responses to invasive bacteria have remained unknown. Here, we report cell type‐dependent microRNA regulations upon infection of mammalian cells with the enteroinvasive pathogen, Typhimurium. Murine macrophages strongly upregulate NF‐κB associated microRNAs; strikingly, these regulations which are induced by bacterial lipopolysaccharide (LPS) occur and persist regardless of successful host invasion and/or replication, or whether an inflammatory response is mounted, suggesting that microRNAs belong to the first line of anti‐bacterial defence. However, a suppression of the global immune regulator miR‐155 in endotoxin‐tolerant macrophages revealed that microRNA responses also depend on the status of infected cells. This study identifies the family as the common denominator of ‐regulated microRNAs in macrophages and epithelial cells, and suggests that repression of relieves cytokine IL‐6 and IL‐10 mRNAs from negative post‐transcriptional control. Our results establish a paradigm of microRNA‐mediated feed‐forward activation of inflammatory factors when mammalian cells are targeted by bacterial pathogens. This study describes the global mammalian micoRNA response to infection and the role of miRNAs in regulating the post‐transcriptional control of inflammatory cytokines.
    Keywords: Il‐10 ; Let‐7 ; Mir‐155 ; Mirna ; Salmonella
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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  • 7
    Language: English
    In: Angewandte Chemie, 03 September 2018, Vol.130(36), pp.11738-11742
    Description: Transgene expression of green fluorescent protein (GFP) has facilitated the spatiotemporal investigation of host–pathogen interactions; however, introduction of the GFP gene remains challenging in drug‐resistant bacteria. Herein, we report a novel far‐red fluorescent nucleic acid stain, , which efficiently labels bacteria through a DNA binding mode without affecting growth and viability. Exemplarily, we stained , a major threat to hospitalized patients, and deciphered divergent interaction strategies of antibiotic‐resistant and antibiotic‐sensitive strains with immune cells. constitutes an off‐the‐shelf reagent for real‐time analysis of bacterial infection, including strains for which the use of genetically encoded reporters is not feasible. Eventually, our approach may aid the development of strategies to combat a major worldwide health threat: multidrug‐resistant bacteria. : Der Fluoreszenzmarker wurde für die Echtzeitanalyse bakterieller Infektionen entwickelt. Dieser tiefrot fluoreszierende Nukleinsäuremarker ermöglichte die effiziente Markierung von Bakterien durch DNA‐Bindung, ohne deren Wachstum oder Lebensfähigkeit zu beeinträchtigen. Anfärben von offenbarte unterschiedliche Interaktionsstrategien von antibiotikaresistenten und ‐sensitiven ‐Stämmen mit Immunzellen.
    Keywords: Antibiotika ; Dna-Erkennung ; Fluoreszenzaktivierte Zellsortierung ; Multiwirkstoffresistente Bakterien ; Tiefrote Cyaninfarbstoffe
    ISSN: 0044-8249
    E-ISSN: 1521-3757
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  • 8
    In: Nature Microbiology, 2016, Vol.2
    Description: Intracellular bacterial pathogens can exhibit large heterogeneity in growth rate inside host cells, with major consequences for the infection outcome. If and how the host responds to this heterogeneity remains poorly understood. Here, we combined a fluorescent reporter of bacterial cell division with single-cell RNA-sequencing analysis to study the macrophage response to different intracellular states of the model pathogen Salmonella enterica serovar Typhimurium. The transcriptomes of individual infected macrophages revealed a spectrum of functional host response states to growing and non-growing bacteria. Intriguingly, macrophages harbouring non-growing Salmonella display hallmarks of the proinflammatory M1 polarization state and differ little from bystander cells, suggesting that non-growing bacteria evade recognition by intracellular immune receptors. By contrast, macrophages containing growing bacteria have turned into an anti-inflammatory, M2-like state, as if fast-growing intracellular Salmonella overcome host defence by reprogramming macrophage polarization. Additionally, our clustering approach reveals intermediate host functional states between these extremes. Altogether, our data suggest that gene expression variability in infected host cells shapes different cellular environments, some of which may favour a growth arrest of Salmonella facilitating immune evasion and the establishment of a long-term niche, while others allow Salmonella to escape intracellular antimicrobial activity and proliferate.
    Keywords: Biology;
    ISBN: 0003971049000
    E-ISSN: 2058-5276
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  • 9
    In: The Journal of Infectious Diseases, 2019, Vol. 219(4), pp.540-543
    Description: MicroRNA miR-17-5p was found to be upregulated in extracellular vesicles in bronchoalveolar lavage fluid from patients with influenza virus–induced acute respiratory distress syndrome and in vesicles of infected lung epithelial cells. It downregulated the expression of the antiviral factor Mx1 and enhanced virus replication. Influenza A virus (IAV) causes severe respiratory infections and alveolar epithelial damage resulting in acute respiratory distress syndrome (ARDS). Extracellular vesicles (EVs) have been shown to mediate cellular crosstalk in inflammation by transfer of microRNAs (miRNAs). In this study, we found significant changes in the miRNA composition of EVs in the bronchoalveolar lavage fluid from patients with IAV-induced ARDS. Among the 9 significantly deregulated microRNAs, miR-17-5p was upregulated in patients’ BALF and in EVs of IAV-infected lung epithelial cells (A549). In these cells, transfer of miR-17-5p strongly downregulated expression of the antiviral factor Mx1 and significantly enhanced IAV replication.
    Keywords: Ards ; Influenza ; Microrna ; Bronchoalveolar Lavage ; Viral Infection
    ISSN: 0022-1899
    E-ISSN: 1537-6613
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  • 10
    Language: English
    In: Methods in molecular biology (Clifton, N.J.), 2019, Vol.1912, pp.3-32
    Description: Inflammatory and infectious diseases are among the main causes of morbidity and mortality worldwide. Inflammation is central to maintenance of organismal homeostasis upon infection, tissue damage, and malignancy. It occurs transiently in response to diverse stimuli (e.g., physical, radioactive, infective, pro-allergenic, or toxic), and in some cases may manifest itself in chronic diseases. To limit the potentially deleterious effects of acute or chronic inflammatory responses, complex transcriptional and posttranscriptional regulatory networks have evolved, often involving nonprotein-coding RNAs (ncRNA). MicroRNAs (miRNAs) are a class of posttranscriptional regulators that control mRNA translation and stability. Long ncRNAs (lncRNAs) are a very diverse group of transcripts 〉200 nt, functioning among others as scaffolds or decoys both in the nucleus and the cytoplasm. By now, it is well established that miRNAs and lncRNAs are implicated in all major cellular processes including control of cell death, proliferation, or metabolism. Extensive research over the last years furthermore revealed a fundamental role of ncRNAs in pathogen recognition and inflammatory responses. This chapter reviews and summarizes the current knowledge on regulatory ncRNA networks in infection and inflammation.
    Keywords: Immunity ; Infection ; Inflammation ; Lncrna ; Mirna
    E-ISSN: 1940-6029
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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