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  1. Article ; Online: Cost-Efficient Transcriptomic-Based Drug Screening.

    Leidner, Jacqueline / Theis, Heidi / Kraut, Michael / Ragogna, Alice / Beyer, Marc / Schultze, Joachim / Schulte-Schrepping, Jonas / Carraro, Caterina / Bonaguro, Lorenzo

    Journal of visualized experiments : JoVE

    2024  , Issue 204

    Abstract: Transcriptomics allows to obtain comprehensive insights into cellular programs and their responses to perturbations. Despite a significant decrease in the costs of library production and sequencing in the last decade, applying these technologies at the ... ...

    Abstract Transcriptomics allows to obtain comprehensive insights into cellular programs and their responses to perturbations. Despite a significant decrease in the costs of library production and sequencing in the last decade, applying these technologies at the scale necessary for drug screening remains prohibitively expensive, obstructing the immense potential of these methods. Our study presents a cost-effective system for transcriptome-based drug screening, combining miniaturized perturbation cultures with mini-bulk transcriptomics. The optimized mini-bulk protocol provides informative biological signals at cost-effective sequencing depth, enabling extensive screening of known drugs and new molecules. Depending on the chosen treatment and incubation time, this protocol will result in sequencing libraries within approximately 2 days. Due to several stopping points within this protocol, the library preparation, as well as the sequencing, can be performed time-independently. Processing simultaneously a high number of samples is possible; measurement of up to 384 samples was tested without loss of data quality. There are also no known limitations to the number of conditions and/or drugs, despite considering variability in optimal drug incubation times.
    MeSH term(s) Transcriptome ; Drug Evaluation, Preclinical ; Gene Expression Profiling ; Gene Library ; Costs and Cost Analysis
    Language English
    Publishing date 2024-02-23
    Publishing country United States
    Document type Journal Article ; Video-Audio Media
    ZDB-ID 2259946-0
    ISSN 1940-087X ; 1940-087X
    ISSN (online) 1940-087X
    ISSN 1940-087X
    DOI 10.3791/65930
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Monocytes and Macrophages in COVID-19.

    Knoll, Rainer / Schultze, Joachim L / Schulte-Schrepping, Jonas

    Frontiers in immunology

    2021  Volume 12, Page(s) 720109

    Abstract: COVID-19 is a contagious viral disease caused by SARS-CoV-2 that led to an ongoing pandemic with massive global health and socioeconomic consequences. The disease is characterized primarily, but not exclusively, by respiratory clinical manifestations ... ...

    Abstract COVID-19 is a contagious viral disease caused by SARS-CoV-2 that led to an ongoing pandemic with massive global health and socioeconomic consequences. The disease is characterized primarily, but not exclusively, by respiratory clinical manifestations ranging from mild common cold symptoms, including cough and fever, to severe respiratory distress and multi-organ failure. Macrophages, a heterogeneous group of yolk-sac derived, tissue-resident mononuclear phagocytes of complex ontogeny present in all mammalian organs, play critical roles in developmental, homeostatic and host defense processes with tissue-dependent plasticity. In case of infection, they are responsible for early pathogen recognition, initiation and resolution of inflammation, as well as repair of tissue damage. Monocytes, bone-marrow derived blood-resident phagocytes, are recruited under pathological conditions such as viral infections to the affected tissue to defend the organism against invading pathogens and to aid in efficient resolution of inflammation. Given their pivotal function in host defense and the potential danger posed by their dysregulated hyperinflammation, understanding monocyte and macrophage phenotypes in COVID-19 is key for tackling the disease's pathological mechanisms. Here, we outline current knowledge on monocytes and macrophages in homeostasis and viral infections and summarize concepts and key findings on their role in COVID-19. While monocytes in the blood of patients with moderate COVID-19 present with an inflammatory, interferon-stimulated gene (ISG)-driven phenotype, cellular dysfunction epitomized by loss of HLA-DR expression and induction of S100 alarmin expression is their dominant feature in severe disease. Pulmonary macrophages in COVID-19 derived from infiltrating inflammatory monocytes are in a hyperactivated state resulting in a detrimental loop of pro-inflammatory cytokine release and recruitment of cytotoxic effector cells thereby exacerbating tissue damage at the site of infection.
    MeSH term(s) COVID-19/immunology ; COVID-19/pathology ; HLA-DR Antigens/immunology ; Humans ; Inflammation/immunology ; Inflammation/pathology ; Macrophages/immunology ; Macrophages/pathology ; Monocytes/immunology ; Monocytes/pathology ; SARS-CoV-2/immunology ; Severity of Illness Index
    Chemical Substances HLA-DR Antigens
    Language English
    Publishing date 2021-07-21
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2021.720109
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: A guide to systems-level immunomics.

    Bonaguro, Lorenzo / Schulte-Schrepping, Jonas / Ulas, Thomas / Aschenbrenner, Anna C / Beyer, Marc / Schultze, Joachim L

    Nature immunology

    2022  Volume 23, Issue 10, Page(s) 1412–1423

    Abstract: The immune system is highly complex and distributed throughout an organism, with hundreds to thousands of cell states existing in parallel with diverse molecular pathways interacting in a highly dynamic and coordinated fashion. Although the ... ...

    Abstract The immune system is highly complex and distributed throughout an organism, with hundreds to thousands of cell states existing in parallel with diverse molecular pathways interacting in a highly dynamic and coordinated fashion. Although the characterization of individual genes and molecules is of the utmost importance for understanding immune-system function, high-throughput, high-resolution omics technologies combined with sophisticated computational modeling and machine-learning approaches are creating opportunities to complement standard immunological methods with new insights into immune-system dynamics. Like systems immunology itself, immunology researchers must take advantage of these technologies and form their own diverse networks, connecting with researchers from other disciplines. This Review is an introduction and 'how-to guide' for immunologists with no particular experience in the field of omics but with the intention to learn about and apply these systems-level approaches, and for immunologists who want to make the most of interdisciplinary networks.
    MeSH term(s) Computer Simulation ; Immune System ; Machine Learning
    Language English
    Publishing date 2022-09-22
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2016987-5
    ISSN 1529-2916 ; 1529-2908
    ISSN (online) 1529-2916
    ISSN 1529-2908
    DOI 10.1038/s41590-022-01309-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Differential impact of high-salt levels in vitro and in vivo on macrophage core functions.

    Müller, Linda / Nasr, Aya Rafea / Jux, Bettina / Makdissi, Nikola / Trowbridge, Justin Wayne / Schmidt, Susanne V / Schultze, Joachim L / Quast, Thomas / Schulte-Schrepping, Jonas / Kolanus, Waldemar / Mass, Elvira

    Molecular biology reports

    2024  Volume 51, Issue 1, Page(s) 343

    Abstract: The consumption of processed food is on the rise leading to huge intake of excess dietary salt, which strongly correlates with development of hypertension, often leading to cardiovascular diseases such as stroke and heart attack, as well as activation of ...

    Abstract The consumption of processed food is on the rise leading to huge intake of excess dietary salt, which strongly correlates with development of hypertension, often leading to cardiovascular diseases such as stroke and heart attack, as well as activation of the immune system. The effect of salt on macrophages is especially interesting as they are able to sense high sodium levels in tissues leading to transcriptional changes. In the skin, macrophages were shown to influence lymphatic vessel growth which, in turn, enables the transport of excess salt and thereby prevents the development of high blood pressure. Furthermore, salt storage in the skin has been linked to the onset of pro-inflammatory effector functions of macrophages in pathogen defence. However, there is only little known about the mechanisms which are involved in changing macrophage function to salt exposure. Here, we characterize the response of macrophages to excess salt both in vitro and in vivo. Our results validate and strengthen the notion that macrophages exhibit chemotactic migration in response to salt gradients in vitro. Furthermore, we demonstrate a reduction in phagocytosis and efferocytosis following acute salt challenge in vitro. While acute exposure to a high-salt diet in vivo has a less pronounced impact on macrophage core functions such as phagocytosis, our data indicate that prolonged salt challenge may exert a distinct effect on the function of macrophages. These findings suggest a potential role for excessive salt sensing by macrophages in the manifestation of diseases related to high-salt diets and explicitly highlight the need for in vivo work to decipher the physiologically relevant impact of excess salt on tissue and cell function.
    MeSH term(s) Humans ; Sodium Chloride, Dietary ; Macrophages ; Sodium Chloride ; Phagocytosis ; Hypertension
    Chemical Substances Sodium Chloride, Dietary ; Sodium Chloride (451W47IQ8X)
    Language English
    Publishing date 2024-02-24
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 186544-4
    ISSN 1573-4978 ; 0301-4851
    ISSN (online) 1573-4978
    ISSN 0301-4851
    DOI 10.1007/s11033-024-09295-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Book ; Online: Severe COVID-19 is marked by a dysregulated myeloid cell compartment. Schulte-Schrepping et al., 2020

    Schulte-Schrepping, J (via Mendeley Data)

    2020  

    Abstract: ... 19 is marked by a dysregulated myeloid cell compartment Jonas Schulte-Schrepping, Nico Reusch ... compartment." Schulte-Schrepping et al., 2020. Table S1 - Cohort details (related to all Figures) Table S2 ...

    Abstract Supplemental tables of the publication "Severe COVID-19 is marked by a dysregulated myeloid cell compartment." Schulte-Schrepping et al., 2020. Table S1 - Cohort details (related to all Figures) Table S2 - Detailed information on antibody panels used for mass cytometry analysis (related to Figure 1,3,6) Table S3 - List of antibodies used for multi-color flow cytometry (related to Figure 1,3,6). Table S4 - Cluster-specific marker gene lists from the scRNA-seq analyses (related to Figure 2,4,5,7 + S2-4,S6) Severe COVID-19 is marked by a dysregulated myeloid cell compartment Jonas Schulte-Schrepping, Nico Reusch, Daniela Paclik, Kevin Baßler, Stephan Schlickeiser, Bowen Zhang, Benjamin Krämer, Tobias Krammer, Sophia Brumhard, Lorenzo Bonaguro, Elena De Domenico, Daniel Wendisch, Martin Grasshoff, Theodore S. Kapellos, Michael Beckstette, Tal Pecht, Adem Saglam, Oliver Dietrich, Henrik E. Mei, Axel R. Schulz, Claudia Conrad, Désirée Kunkel, Ehsan Vafadarnejad, Cheng-Jian Xu, Arik Horne, Miriam Herbert, Anna Drews, Charlotte Thibeault, Moritz Pfeiffer, Stefan Hippenstiel, Andreas Hocke, Holger Müller-Redetzky, Katrin-Moira Heim, Felix Machleidt, Alexander Uhrig, Laure Bosquillon de Jarcy, Linda Jürgens, Miriam Stegemann, Christoph R. Glösenkamp, Hans-Dieter Volk, Christine Goffinet, Markus Landthaler, Emanuel Wyler, Philipp Georg, Maria Schneider, Chantip Dang-Heine, Nick Neuwinger, Kai Kappert, Rudolf Tauber, Victor Corman, Jan Raabe, Kim Melanie Kaiser, Michael To Vinh, Gereon Rieke, Christian Meisel, Thomas Ulas, Matthias Becker, Robert Geffers, Martin Witzenrath, Christian Drosten, Norbert Suttorp, Christof von Kalle, Florian Kurth, Kristian Händler, Joachim L. Schultze, Anna C Aschenbrenner, Yang Li, Jacob Nattermann, Birgit Sawitzki, Antoine-Emmanuel Saliba, Leif Erik Sander, Deutsche COVID-19 OMICS Initiative (DeCOI) Coronavirus Disease 2019 (COVID-19) is a mild to moderate respiratory tract infection, however, a subset of patients progresses to severe disease and respiratory failure. The mechanism of protective immunity in mild forms and the pathogenesis of severe COVID-19, associated with increased neutrophil counts and dysregulated immune responses, remains unclear. In a dual-center, two-cohort study, we combined single-cell RNA-sequencing and single-cell proteomics of whole blood and peripheral blood mononuclear cells to determine changes in immune cell composition and activation in mild vs. severe COVID-19 (242 samples from 109 individuals) over time. HLA-DR high CD11c high inflammatory monocytes with an interferon-stimulated gene signature were elevated in mild COVID-19. Severe COVID-19 was marked by occurrence of neutrophil precursors, as evidence of emergency myelopoiesis, dysfunctional mature neutrophils, and HLA-DR low monocytes. Our study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and it reveals profound alterations in the myeloid cell compartment associated with severe COVID-19.
    Keywords Interdisciplinary sciences ; covid19
    Publishing date 2020-07-28T12:16:59.477Z
    Publishing country nl
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article: Einzelzell-Epigenomik des Immunsystems

    Schulte-Schrepping, Jonas / Aschenbrenner, Anna C. / Schultze, Joachim L.

    Immunologie

    2019  Volume 3, Issue 4, Page(s) 254

    Language German
    Document type Article
    ZDB-ID 2935137-6
    ISSN 2625-3585 ; 2513-1583
    Database Current Contents Medicine

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  7. Article ; Online: Neutrophils in COVID-19.

    Reusch, Nico / De Domenico, Elena / Bonaguro, Lorenzo / Schulte-Schrepping, Jonas / Baßler, Kevin / Schultze, Joachim L / Aschenbrenner, Anna C

    Frontiers in immunology

    2021  Volume 12, Page(s) 652470

    Abstract: Strong evidence has been accumulated since the beginning of the COVID-19 pandemic that neutrophils play an important role in the pathophysiology, particularly in those with severe disease courses. While originally considered to be a rather homogeneous ... ...

    Abstract Strong evidence has been accumulated since the beginning of the COVID-19 pandemic that neutrophils play an important role in the pathophysiology, particularly in those with severe disease courses. While originally considered to be a rather homogeneous cell type, recent attention to neutrophils has uncovered their fascinating transcriptional and functional diversity as well as their developmental trajectories. These new findings are important to better understand the many facets of neutrophil involvement not only in COVID-19 but also many other acute or chronic inflammatory diseases, both communicable and non-communicable. Here, we highlight the observed immune deviation of neutrophils in COVID-19 and summarize several promising therapeutic attempts to precisely target neutrophils and their reactivity in patients with COVID-19.
    MeSH term(s) COVID-19/epidemiology ; COVID-19/immunology ; Humans ; Neutrophils/immunology ; Pandemics ; SARS-CoV-2/immunology
    Language English
    Publishing date 2021-03-25
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2021.652470
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: A Bioinformatic Toolkit for Single-Cell mRNA Analysis.

    Baßler, Kevin / Günther, Patrick / Schulte-Schrepping, Jonas / Becker, Matthias / Biernat, Paweł

    Methods in molecular biology (Clifton, N.J.)

    2019  Volume 1979, Page(s) 433–455

    Abstract: The recent technological developments in the field of single-cell RNA-Seq enable us to assay the transcriptome of up to a million single cells in parallel. However, the analyses of such big datasets present a major challenge. During the last decade, a ... ...

    Abstract The recent technological developments in the field of single-cell RNA-Seq enable us to assay the transcriptome of up to a million single cells in parallel. However, the analyses of such big datasets present a major challenge. During the last decade, a wide variety of strategies have been proposed covering different steps of the analysis. Here, we introduce a selection of computational tools to provide an overview of a generic analysis pipeline.The first step of every scRNA-Seq experiment is proper study design, which does not require sophisticated experimental or informatics skills but is nonetheless presumably the most important step. The quality of the resulting data strictly depends on the proper planning of the experiment, including the selection of the most suitable technology for the biological question of interest as well as an elaborated study design to minimize the influence of confounding factors. Once the experiment has been conducted, the raw sequencing data needs to be processed to extract the gene expression information for each cell. This task comprises quality assessment of the sequenced reads, alignment against a reference genome, demultiplexing of the cell barcodes, and quantification of the reads/transcripts per gene. As any other transcriptomics technology, single-cell mRNA-Seq requires data normalization to assure sample-to-sample, here cell-to-cell, comparability and the consideration of confounding factors.Once gene expression values have been extracted from the reads and normalized, the researcher has the agony of choosing between a plethora of analysis approaches to investigate diverse aspects of the single-cell transcriptomes, such as dimensionality reduction and clustering to explore cellular heterogeneity or trajectory analysis to model differentiation processes.In this chapter, we present a wrap-up of the abovementioned steps to conduct single-cell RNA-Seq analyses and present a selection of existing tools.
    MeSH term(s) Animals ; Cluster Analysis ; Gene Expression Profiling/methods ; Genomics/methods ; Humans ; Quality Control ; RNA, Messenger/genetics ; Sequence Analysis, RNA/methods ; Single-Cell Analysis/methods ; Software ; Transcriptome
    Chemical Substances RNA, Messenger
    Language English
    Publishing date 2019-04-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-9240-9_26
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: The Myeloid Cell Compartment-Cell by Cell.

    Bassler, Kevin / Schulte-Schrepping, Jonas / Warnat-Herresthal, Stefanie / Aschenbrenner, Anna C / Schultze, Joachim L

    Annual review of immunology

    2019  Volume 37, Page(s) 269–293

    Abstract: Myeloid cells are a major cellular compartment of the immune system comprising monocytes, dendritic cells, tissue macrophages, and granulocytes. Models of cellular ontogeny, activation, differentiation, and tissue-specific functions of myeloid cells have ...

    Abstract Myeloid cells are a major cellular compartment of the immune system comprising monocytes, dendritic cells, tissue macrophages, and granulocytes. Models of cellular ontogeny, activation, differentiation, and tissue-specific functions of myeloid cells have been revisited during the last years with surprising results; for example, most tissue macrophages are yolk sac derived, monocytes and macrophages follow a multidimensional model of activation, and tissue signals have a significant impact on the functionality of all these cells. While these exciting results have brought these cells back to center stage, their enormous plasticity and heterogeneity, during both homeostasis and disease, are far from understood. At the same time, the ongoing revolution in single-cell genomics, with single-cell RNA sequencing (scRNA-seq) leading the way, promises to change this. Prevailing models of hematopoiesis with distinct intermediates are challenged by scRNA-seq data suggesting more continuous developmental trajectories in the myeloid cell compartment. Cell subset structures previously defined by protein marker expression need to be revised based on unbiased analyses of scRNA-seq data. Particularly in inflammatory conditions, myeloid cells exhibit substantially vaster heterogeneity than previously anticipated, and work performed within large international projects, such as the Human Cell Atlas, has already revealed novel tissue macrophage subsets. Based on these exciting developments, we propose the next steps to a full understanding of the myeloid cell compartment in health and diseases.
    MeSH term(s) Animals ; Biomarkers ; Cell Differentiation ; Cell Plasticity ; Cellular Microenvironment ; Homeostasis ; Humans ; Inflammation/immunology ; Myeloid Cells/physiology ; Sequence Analysis, RNA
    Chemical Substances Biomarkers
    Language English
    Publishing date 2019-01-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 604953-9
    ISSN 1545-3278 ; 0732-0582
    ISSN (online) 1545-3278
    ISSN 0732-0582
    DOI 10.1146/annurev-immunol-042718-041728
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Optimized workflow for single-cell transcriptomics on infectious diseases including COVID-19.

    De Domenico, Elena / Bonaguro, Lorenzo / Schulte-Schrepping, Jonas / Becker, Matthias / Händler, Kristian / Schultze, Joachim L

    STAR protocols

    2020  Volume 1, Issue 3, Page(s) 100233

    Abstract: ... of this protocol, please refer to Schulte-Schrepping et al. (2020). ...

    Abstract In December 2019, a new coronavirus, SARS-CoV-2, which causes the respiratory illness that led to the COVID-19 pandemic, was reported. In the face of such a new pathogen, special precautions must be taken to examine potentially infectious materials due to the lack of knowledge on disease transmissibility, infectivity, and molecular pathogenicity. Here, we present a complete and safe workflow for performing scRNA-seq experiments on blood samples of infected patients from cell isolation to data analysis using the micro-well based BD Rhapsody platform. For complete information on the use and execution of this protocol, please refer to Schulte-Schrepping et al. (2020).
    MeSH term(s) Biomarkers/blood ; COVID-19/genetics ; COVID-19/metabolism ; Communicable Diseases/genetics ; Communicable Diseases/metabolism ; Humans ; RNA-Seq/methods ; SARS-CoV-2 ; Single-Cell Analysis/methods ; Transcriptome/genetics ; Workflow
    Chemical Substances Biomarkers
    Language English
    Publishing date 2020-12-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2020.100233
    Database MEDical Literature Analysis and Retrieval System OnLINE

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