1
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Figueroa KP, Gross C, Buena-Atienza E, Paul S, Gandelman M, Kakar N, Sturm M, Casadei N, Admard J, Park J, Zühlke C, Hellenbroich Y, Pozojevic J, Balachandran S, Händler K, Zittel S, Timmann D, Erdlenbruch F, Herrmann L, Feindt T, Zenker M, Klopstock T, Dufke C, Scoles DR, Koeppen A, Spielmann M, Riess O, Ossowski S, Haack TB, Pulst SM. A GGC-repeat expansion in ZFHX3 encoding polyglycine causes spinocerebellar ataxia type 4 and impairs autophagy. Nat Genet 2024:10.1038/s41588-024-01719-5. [PMID: 38684900 DOI: 10.1038/s41588-024-01719-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/18/2024] [Indexed: 05/02/2024]
Abstract
Despite linkage to chromosome 16q in 1996, the mutation causing spinocerebellar ataxia type 4 (SCA4), a late-onset sensory and cerebellar ataxia, remained unknown. Here, using long-read single-strand whole-genome sequencing (LR-GS), we identified a heterozygous GGC-repeat expansion in a large Utah pedigree encoding polyglycine (polyG) in zinc finger homeobox protein 3 (ZFHX3), also known as AT-binding transcription factor 1 (ATBF1). We queried 6,495 genome sequencing datasets and identified the repeat expansion in seven additional pedigrees. Ultrarare DNA variants near the repeat expansion indicate a common distant founder event in Sweden. Intranuclear ZFHX3-p62-ubiquitin aggregates were abundant in SCA4 basis pontis neurons. In fibroblasts and induced pluripotent stem cells, the GGC expansion led to increased ZFHX3 protein levels and abnormal autophagy, which were normalized with small interfering RNA-mediated ZFHX3 knockdown in both cell types. Improving autophagy points to a therapeutic avenue for this novel polyG disease. The coding GGC-repeat expansion in an extremely G+C-rich region was not detectable by short-read whole-exome sequencing, which demonstrates the power of LR-GS for variant discovery.
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Affiliation(s)
- Karla P Figueroa
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
| | - Caspar Gross
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
| | - Elena Buena-Atienza
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
| | - Sharan Paul
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
| | - Mandi Gandelman
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
| | - Naseebullah Kakar
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
- Department of Biotechnology, FLS&I, BUITEMS, Quetta, Pakistan
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
| | - Joohyun Park
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Christine Zühlke
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Yorck Hellenbroich
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Jelena Pozojevic
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Saranya Balachandran
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Kristian Händler
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Simone Zittel
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dagmar Timmann
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), Essen University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Friedrich Erdlenbruch
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), Essen University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Laura Herrmann
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg and Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Thomas Klopstock
- Department of Neurology with Friedrich-Baur-Institute, University Hospital of Ludwig-Maximilians-Universität München, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Claudia Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Daniel R Scoles
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
| | | | - Malte Spielmann
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg, Lübeck, Kiel, Lübeck, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- NGS Competence Center Tübingen, Tübingen, Germany.
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
| | - Stefan M Pulst
- Department of Neurology, University of Utah, Salt Lake City, UT, USA.
- Clinical Neurosciences Center, University of Utah Hospitals and Clinics, Salt Lake City, UT, USA.
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Wenner N, Zhu X, Rowe WPM, Händler K, Hinton JCD. Succinate utilisation by Salmonella is inhibited by multiple regulatory systems. PLoS Genet 2024; 20:e1011142. [PMID: 38457455 DOI: 10.1371/journal.pgen.1011142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/26/2024] [Accepted: 01/19/2024] [Indexed: 03/10/2024] Open
Abstract
Succinate is a potent immune signalling molecule that is present in the mammalian gut and within macrophages. Both of these infection niches are colonised by the pathogenic bacterium Salmonella enterica serovar Typhimurium during infection. Succinate is a C4-dicarboyxlate that can serve as a source of carbon for bacteria. When succinate is provided as the sole carbon source for in vitro cultivation, Salmonella and other enteric bacteria exhibit a slow growth rate and a long lag phase. This growth inhibition phenomenon was known to involve the sigma factor RpoS, but the genetic basis of the repression of bacterial succinate utilisation was poorly understood. Here, we use an experimental evolution approach to isolate fast-growing mutants during growth of S. Typhimurium on succinate containing minimal medium. Our approach reveals novel RpoS-independent systems that inhibit succinate utilisation. The CspC RNA binding protein restricts succinate utilisation, an inhibition that is antagonised by high levels of the small regulatory RNA (sRNA) OxyS. We discovered that the Fe-S cluster regulatory protein IscR inhibits succinate utilisation by repressing the C4-dicarboyxlate transporter DctA. Furthermore, the ribose operon repressor RbsR is required for the complete RpoS-driven repression of succinate utilisation, suggesting a novel mechanism of RpoS regulation. Our discoveries shed light on the redundant regulatory systems that tightly regulate the utilisation of succinate. We speculate that the control of central carbon metabolism by multiple regulatory systems in Salmonella governs the infection niche-specific utilisation of succinate.
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Affiliation(s)
- Nicolas Wenner
- Clinical Infection, Microbiology & Immunology, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Xiaojun Zhu
- Clinical Infection, Microbiology & Immunology, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Will P M Rowe
- Clinical Infection, Microbiology & Immunology, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Kristian Händler
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Jay C D Hinton
- Clinical Infection, Microbiology & Immunology, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
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3
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Knoll R, Bonaguro L, dos Santos JC, Warnat-Herresthal S, Jacobs-Cleophas MCP, Blümel E, Reusch N, Horne A, Herbert M, Nuesch-Germano M, Otten T, van der Heijden WA, van de Wijer L, Shalek AK, Händler K, Becker M, Beyer MD, Netea MG, Joosten LAB, van der Ven AJAM, Schultze JL, Aschenbrenner AC. Identification of drug candidates targeting monocyte reprogramming in people living with HIV. Front Immunol 2023; 14:1275136. [PMID: 38077315 PMCID: PMC10703486 DOI: 10.3389/fimmu.2023.1275136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/18/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction People living with HIV (PLHIV) are characterized by functional reprogramming of innate immune cells even after long-term antiretroviral therapy (ART). In order to assess technical feasibility of omics technologies for application to larger cohorts, we compared multiple omics data layers. Methods Bulk and single-cell transcriptomics, flow cytometry, proteomics, chromatin landscape analysis by ATAC-seq as well as ex vivo drug stimulation were performed in a small number of blood samples derived from PLHIV and healthy controls from the 200-HIV cohort study. Results Single-cell RNA-seq analysis revealed that most immune cells in peripheral blood of PLHIV are altered in their transcriptomes and that a specific functional monocyte state previously described in acute HIV infection is still existing in PLHIV while other monocyte cell states are only occurring acute infection. Further, a reverse transcriptome approach on a rather small number of PLHIV was sufficient to identify drug candidates for reversing the transcriptional phenotype of monocytes in PLHIV. Discussion These scientific findings and technological advancements for clinical application of single-cell transcriptomics form the basis for the larger 2000-HIV multicenter cohort study on PLHIV, for which a combination of bulk and single-cell transcriptomics will be included as the leading technology to determine disease endotypes in PLHIV and to predict disease trajectories and outcomes.
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Affiliation(s)
- Rainer Knoll
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Jéssica C. dos Santos
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Stefanie Warnat-Herresthal
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Maartje C. P. Jacobs-Cleophas
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Edda Blümel
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Nico Reusch
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Arik Horne
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Systems Hematology, Stem Cells & Precision Medicine, Max Delbrück Center - Berlin Institute for Medical Systems Biology (MDCBIMSB), Berlin, Germany
| | - Miriam Herbert
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- In Vivo Cell Biology of Infection, Max Planck Institute for Infection Biology (MPIIB), Berlin, Germany
| | - Melanie Nuesch-Germano
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Twan Otten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Wouter A. van der Heijden
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Lisa van de Wijer
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alex K. Shalek
- Broad Institute at Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, United States
- Ragon Institute of Mass General Hospital (MGH), MIT, and Harvard, Cambridge, MA, United States
- Department of Chemistry, Institute for Medical Engineering and Science, Koch Institute, Cambridge, MA, United States
| | - Kristian Händler
- Platform for Single Cell Genomics and Epigenomics (PRECISE), DZNE and University of Bonn, Bonn, Germany
- Institute for Human Genetics, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Matthias Becker
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Marc D. Beyer
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Platform for Single Cell Genomics and Epigenomics (PRECISE), DZNE and University of Bonn, Bonn, Germany
| | - Mihai G. Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
- Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Leo A. B. Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Andre J. A. M. van der Ven
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Joachim L. Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
- Platform for Single Cell Genomics and Epigenomics (PRECISE), DZNE and University of Bonn, Bonn, Germany
| | - Anna C. Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
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4
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Kapellos TS, Baßler K, Fujii W, Nalkurthi C, Schaar AC, Bonaguro L, Pecht T, Galvao I, Agrawal S, Saglam A, Dudkin E, Frishberg A, de Domenico E, Horne A, Donovan C, Kim RY, Gallego-Ortega D, Gillett TE, Ansari M, Schulte-Schrepping J, Offermann N, Antignano I, Sivri B, Lu W, Eapen MS, van Uelft M, Osei-Sarpong C, van den Berge M, Donker HC, Groen HJM, Sohal SS, Klein J, Schreiber T, Feißt A, Yildirim AÖ, Schiller HB, Nawijn MC, Becker M, Händler K, Beyer M, Capasso M, Ulas T, Hasenauer J, Pizarro C, Theis FJ, Hansbro PM, Skowasch D, Schultze JL. Systemic alterations in neutrophils and their precursors in early-stage chronic obstructive pulmonary disease. Cell Rep 2023; 42:112525. [PMID: 37243592 PMCID: PMC10320832 DOI: 10.1016/j.celrep.2023.112525] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/18/2023] [Accepted: 05/01/2023] [Indexed: 05/29/2023] Open
Abstract
Systemic inflammation is established as part of late-stage severe lung disease, but molecular, functional, and phenotypic changes in peripheral immune cells in early disease stages remain ill defined. Chronic obstructive pulmonary disease (COPD) is a major respiratory disease characterized by small-airway inflammation, emphysema, and severe breathing difficulties. Using single-cell analyses we demonstrate that blood neutrophils are already increased in early-stage COPD, and changes in molecular and functional neutrophil states correlate with lung function decline. Assessing neutrophils and their bone marrow precursors in a murine cigarette smoke exposure model identified similar molecular changes in blood neutrophils and precursor populations that also occur in the blood and lung. Our study shows that systemic molecular alterations in neutrophils and their precursors are part of early-stage COPD, a finding to be further explored for potential therapeutic targets and biomarkers for early diagnosis and patient stratification.
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Affiliation(s)
- Theodore S Kapellos
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; Comprehensive Pneumology Center (CPC), Institute of Lung Health and Immunity (LHI), Member of the German Center for Lung Research (DZL), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Kevin Baßler
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Wataru Fujii
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Christina Nalkurthi
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW 2007, Australia
| | - Anna C Schaar
- Institute of Computational Biology (ICB), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Department of Mathematics, Technische Universität München, 85748 Garching, Germany
| | - Lorenzo Bonaguro
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; Platform for Single Cell Genomics and Epigenomics (PRECISE), German Center for Neurodegenerative Diseases and the University of Bonn, 53127 Bonn, Germany
| | - Tal Pecht
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Izabela Galvao
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW 2007, Australia
| | - Shobhit Agrawal
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Adem Saglam
- Platform for Single Cell Genomics and Epigenomics (PRECISE), German Center for Neurodegenerative Diseases and the University of Bonn, 53127 Bonn, Germany
| | - Erica Dudkin
- Computational Life Sciences, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Amit Frishberg
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; Institute of Computational Biology (ICB), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Elena de Domenico
- Platform for Single Cell Genomics and Epigenomics (PRECISE), German Center for Neurodegenerative Diseases and the University of Bonn, 53127 Bonn, Germany
| | - Arik Horne
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Chantal Donovan
- University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW 2007, Australia; Immune Health, Hunter Medical Research Institute, New Lambton and The University of Newcastle, Newcastle, NSW 2305, Australia
| | - Richard Y Kim
- University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW 2007, Australia; Immune Health, Hunter Medical Research Institute, New Lambton and The University of Newcastle, Newcastle, NSW 2305, Australia
| | - David Gallego-Ortega
- School of Biomedical Engineering, Faculty of Engineering and IT, University of Technology Sydney, Garvan Institute of Medical Research, and St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2010, Australia
| | - Tessa E Gillett
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 AB Groningen, the Netherlands; GRIAC Research Institute, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Meshal Ansari
- Comprehensive Pneumology Center (CPC), Institute of Lung Health and Immunity (LHI), Member of the German Center for Lung Research (DZL), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Computational Biology (ICB), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jonas Schulte-Schrepping
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Nina Offermann
- Immunregulation, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Ignazio Antignano
- Immunregulation, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Burcu Sivri
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Wenying Lu
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, 7250 TAS, Australia
| | - Mathew S Eapen
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, 7250 TAS, Australia
| | - Martina van Uelft
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Collins Osei-Sarpong
- Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Maarten van den Berge
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 AB Groningen, the Netherlands; Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands
| | - Hylke C Donker
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 AB Groningen, the Netherlands; Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands
| | - Harry J M Groen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 AB Groningen, the Netherlands; Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands
| | - Sukhwinder S Sohal
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, 7250 TAS, Australia
| | - Johanna Klein
- Department of Internal Medicine II, Pneumology, University Hospital Bonn, 53127 Bonn, Germany
| | - Tina Schreiber
- Department of Internal Medicine II, Pneumology, University Hospital Bonn, 53127 Bonn, Germany
| | - Andreas Feißt
- University Clinics for Radiology, University Hospital Bonn, 53127 Bonn, Germany
| | - Ali Önder Yildirim
- Comprehensive Pneumology Center (CPC), Institute of Lung Health and Immunity (LHI), Member of the German Center for Lung Research (DZL), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Herbert B Schiller
- Comprehensive Pneumology Center (CPC), Institute of Lung Health and Immunity (LHI), Member of the German Center for Lung Research (DZL), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Martijn C Nawijn
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 AB Groningen, the Netherlands; GRIAC Research Institute, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Matthias Becker
- Modular HPC and AI, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Kristian Händler
- Platform for Single Cell Genomics and Epigenomics (PRECISE), German Center for Neurodegenerative Diseases and the University of Bonn, 53127 Bonn, Germany; Institute of Human Genetics, University of Lübeck, 23562 Lübeck, Germany
| | - Marc Beyer
- Platform for Single Cell Genomics and Epigenomics (PRECISE), German Center for Neurodegenerative Diseases and the University of Bonn, 53127 Bonn, Germany; Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Melania Capasso
- Immunregulation, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Thomas Ulas
- Platform for Single Cell Genomics and Epigenomics (PRECISE), German Center for Neurodegenerative Diseases and the University of Bonn, 53127 Bonn, Germany
| | - Jan Hasenauer
- Institute of Computational Biology (ICB), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Department of Mathematics, Technische Universität München, 85748 Garching, Germany; Computational Life Sciences, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Carmen Pizarro
- Department of Internal Medicine II, Pneumology, University Hospital Bonn, 53127 Bonn, Germany
| | - Fabian J Theis
- Institute of Computational Biology (ICB), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Department of Mathematics, Technische Universität München, 85748 Garching, Germany
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW 2007, Australia; University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW 2007, Australia
| | - Dirk Skowasch
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, 7250 TAS, Australia
| | - Joachim L Schultze
- Comprehensive Pneumology Center (CPC), Institute of Lung Health and Immunity (LHI), Member of the German Center for Lung Research (DZL), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Department of Mathematics, Technische Universität München, 85748 Garching, Germany.
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5
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Katzmarski N, Domínguez-Andrés J, Cirovic B, Renieris G, Ciarlo E, Le Roy D, Lepikhov K, Kattler K, Gasparoni G, Händler K, Theis H, Beyer M, van der Meer JWM, Joosten LAB, Walter J, Schultze JL, Roger T, Giamarellos-Bourboulis EJ, Schlitzer A, Netea MG. Author Correction: Transmission of trained immunity and heterologous resistance to infections across generations. Nat Immunol 2023; 24:371-372. [PMID: 36653441 DOI: 10.1038/s41590-023-01426-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Natalie Katzmarski
- Quantitative Systems Biology, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Jorge Domínguez-Andrés
- Department of Internal Medicine and Radboud Center for Infectious diseases, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands. .,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Branko Cirovic
- Quantitative Systems Biology, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Georgios Renieris
- Department 4th of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Eleonora Ciarlo
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
| | - Didier Le Roy
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
| | - Konstantin Lepikhov
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Kathrin Kattler
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Gilles Gasparoni
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Kristian Händler
- Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Heidi Theis
- Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Marc Beyer
- Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany.,Molecular Immunology in Neurodegeneration, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Jos W M van der Meer
- Department of Internal Medicine and Radboud Center for Infectious diseases, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious diseases, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jörn Walter
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Joachim L Schultze
- Molecular Immunology in Neurodegeneration, German Center for Neurodegenerative Diseases, Bonn, Germany.,Department for Genomics & Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Thierry Roger
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
| | | | - Andreas Schlitzer
- Quantitative Systems Biology, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious diseases, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.,Department for Immunology & Metabolism, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
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6
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Bonaguro L, Schulte-Schrepping J, Carraro C, Sun LL, Reiz B, Gemünd I, Saglam A, Rahmouni S, Georges M, Arts P, Hoischen A, Joosten LA, van de Veerdonk FL, Netea MG, Händler K, Mukherjee S, Ulas T, Schultze JL, Aschenbrenner AC. Human variation in population-wide gene expression data predicts gene perturbation phenotype. iScience 2022; 25:105328. [PMID: 36310583 PMCID: PMC9614568 DOI: 10.1016/j.isci.2022.105328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/13/2022] [Accepted: 10/07/2022] [Indexed: 11/24/2022] Open
Abstract
Population-scale datasets of healthy individuals capture genetic and environmental factors influencing gene expression. The expression variance of a gene of interest (GOI) can be exploited to set up a quasi loss- or gain-of-function "in population" experiment. We describe here an approach, huva (human variation), taking advantage of population-scale multi-layered data to infer gene function and relationships between phenotypes and expression. Within a reference dataset, huva derives two experimental groups with LOW or HIGH expression of the GOI, enabling the subsequent comparison of their transcriptional profile and functional parameters. We demonstrate that this approach robustly identifies the phenotypic relevance of a GOI allowing the stratification of genes according to biological functions, and we generalize this concept to almost 16,000 genes in the human transcriptome. Additionally, we describe how huva predicts monocytes to be the major cell type in the pathophysiology of STAT1 mutations, evidence validated in a clinical cohort.
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Affiliation(s)
- Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
| | - Jonas Schulte-Schrepping
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
| | - Caterina Carraro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Laura L. Sun
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
| | | | - Ioanna Gemünd
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, 3010 VIC, Australia
| | - Adem Saglam
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
| | - Souad Rahmouni
- Unit of Animal Genomics, GIGA-Institute, University of Liège, 4000 Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA-Institute, University of Liège, 4000 Liège, Belgium
| | - Peer Arts
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, 5000 SA, Australia
| | - Alexander Hoischen
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Leo A.B. Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
- Department of Medical Genetics, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Frank L. van de Veerdonk
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
- Immunology and Metabolism, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
| | - Kristian Händler
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, 53127 Bonn, Germany
| | - Sach Mukherjee
- Statistics and Machine Learning, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK
| | - Thomas Ulas
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, 53127 Bonn, Germany
| | - Joachim L. Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, 53127 Bonn, Germany
| | - Anna C. Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
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7
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Wischhof L, Lee H, Tutas J, Overkott C, Tedt E, Stork M, Peitz M, Brüstle O, Ulas T, Händler K, Schultze JL, Ehninger D, Nicotera P, Salomoni P, Bano D. BCL7A-containing SWI/SNF/BAF complexes modulate mitochondrial bioenergetics during neural progenitor differentiation. EMBO J 2022; 41:e110595. [PMID: 36305367 PMCID: PMC9713712 DOI: 10.15252/embj.2022110595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/21/2022] [Accepted: 10/07/2022] [Indexed: 01/15/2023] Open
Abstract
Mammalian SWI/SNF/BAF chromatin remodeling complexes influence cell lineage determination. While the contribution of these complexes to neural progenitor cell (NPC) proliferation and differentiation has been reported, little is known about the transcriptional profiles that determine neurogenesis or gliogenesis. Here, we report that BCL7A is a modulator of the SWI/SNF/BAF complex that stimulates the genome-wide occupancy of the ATPase subunit BRG1. We demonstrate that BCL7A is dispensable for SWI/SNF/BAF complex integrity, whereas it is essential to regulate Notch/Wnt pathway signaling and mitochondrial bioenergetics in differentiating NPCs. Pharmacological stimulation of Wnt signaling restores mitochondrial respiration and attenuates the defective neurogenic patterns observed in NPCs lacking BCL7A. Consistently, treatment with an enhancer of mitochondrial biogenesis, pioglitazone, partially restores mitochondrial respiration and stimulates neuronal differentiation of BCL7A-deficient NPCs. Using conditional BCL7A knockout mice, we reveal that BCL7A expression in NPCs and postmitotic neurons is required for neuronal plasticity and supports behavioral and cognitive performance. Together, our findings define the specific contribution of BCL7A-containing SWI/SNF/BAF complexes to mitochondria-driven NPC commitment, thereby providing a better understanding of the cell-intrinsic transcriptional processes that connect metabolism, neuronal morphogenesis, and cognitive flexibility.
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Affiliation(s)
- Lena Wischhof
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Hang‐Mao Lee
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Janine Tutas
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | | | - Eileen Tedt
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Miriam Stork
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Michael Peitz
- Institute of Reconstructive NeurobiologyUniversity of Bonn Medical Faculty and University Hospital BonnBonnGermany,Cell Programming Core FacilityUniversity of Bonn Medical FacultyBonnGermany
| | - Oliver Brüstle
- Institute of Reconstructive NeurobiologyUniversity of Bonn Medical Faculty and University Hospital BonnBonnGermany
| | - Thomas Ulas
- PRECISE Platform for Single Cell Genomics and EpigenomicsGerman Center for Neurodegenerative Diseases (DZNE) and the University of BonnBonnGermany
| | - Kristian Händler
- PRECISE Platform for Single Cell Genomics and EpigenomicsGerman Center for Neurodegenerative Diseases (DZNE) and the University of BonnBonnGermany
| | - Joachim L Schultze
- PRECISE Platform for Single Cell Genomics and EpigenomicsGerman Center for Neurodegenerative Diseases (DZNE) and the University of BonnBonnGermany,Department for Genomics and Immunoregulation, LIMES InstituteUniversity of BonnBonnGermany
| | - Dan Ehninger
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | | | - Paolo Salomoni
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Daniele Bano
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
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8
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Hansen JN, Kaiser F, Leyendecker P, Stüven B, Krause JH, Derakhshandeh F, Irfan J, Sroka TJ, Preval KM, Desai PB, Kraut M, Theis H, Drews AD, De-Domenico E, Händler K, Pazour GJ, Henderson DJP, Mick DU, Wachten D. A cAMP signalosome in primary cilia drives gene expression and kidney cyst formation. EMBO Rep 2022; 23:e54315. [PMID: 35695071 PMCID: PMC9346484 DOI: 10.15252/embr.202154315] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 05/11/2022] [Accepted: 05/19/2022] [Indexed: 12/22/2022] Open
Abstract
The primary cilium constitutes an organelle that orchestrates signal transduction independently from the cell body. Dysregulation of this intricate molecular architecture leads to severe human diseases, commonly referred to as ciliopathies. However, the molecular underpinnings how ciliary signaling orchestrates a specific cellular output remain elusive. By combining spatially resolved optogenetics with RNA sequencing and imaging, we reveal a novel cAMP signalosome that is functionally distinct from the cytoplasm. We identify the genes and pathways targeted by the ciliary cAMP signalosome and shed light on the underlying mechanisms and downstream signaling. We reveal that chronic stimulation of the ciliary cAMP signalosome transforms kidney epithelia from tubules into cysts. Counteracting this chronic cAMP elevation in the cilium by small molecules targeting activation of phosphodiesterase‐4 long isoforms inhibits cyst growth. Thereby, we identify a novel concept of how the primary cilium controls cellular functions and maintains tissue integrity in a specific and spatially distinct manner and reveal novel molecular components that might be involved in the development of one of the most common genetic diseases, polycystic kidney disease.
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Affiliation(s)
- Jan N Hansen
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Fabian Kaiser
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Philipp Leyendecker
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Birthe Stüven
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Jens-Henning Krause
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | | | | | - Tommy J Sroka
- Center for Molecular Signaling (PZMS), Center of Human and Molecular Biology (ZHMB), Saarland University, School of Medicine, Homburg, Germany
| | - Kenley M Preval
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Biotech II, Worcester, MA, USA
| | - Paurav B Desai
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Biotech II, Worcester, MA, USA
| | - Michael Kraut
- Precise Platform for Single Cell Genomics and Epigenomics, Department of Systems Medicine, German Center for Neurogenerative Diseases, Bonn, Germany
| | - Heidi Theis
- Precise Platform for Single Cell Genomics and Epigenomics, Department of Systems Medicine, German Center for Neurogenerative Diseases, Bonn, Germany
| | - Anna-Dorothee Drews
- Precise Platform for Single Cell Genomics and Epigenomics, Department of Systems Medicine, German Center for Neurogenerative Diseases, Bonn, Germany
| | - Elena De-Domenico
- Precise Platform for Single Cell Genomics and Epigenomics, Department of Systems Medicine, German Center for Neurogenerative Diseases, Bonn, Germany
| | - Kristian Händler
- Precise Platform for Single Cell Genomics and Epigenomics, Department of Systems Medicine, German Center for Neurogenerative Diseases, Bonn, Germany
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Biotech II, Worcester, MA, USA
| | | | - David U Mick
- Center for Molecular Signaling (PZMS), Center of Human and Molecular Biology (ZHMB), Saarland University, School of Medicine, Homburg, Germany
| | - Dagmar Wachten
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
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9
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Baßler K, Fujii W, Kapellos TS, Dudkin E, Reusch N, Horne A, Reiz B, Luecken MD, Osei-Sarpong C, Warnat-Herresthal S, Bonaguro L, Schulte-Schrepping J, Wagner A, Günther P, Pizarro C, Schreiber T, Knoll R, Holsten L, Kröger C, De Domenico E, Becker M, Händler K, Wohnhaas CT, Baumgartner F, Köhler M, Theis H, Kraut M, Wadsworth MH, Hughes TK, Ferreira HJ, Hinkley E, Kaltheuner IH, Geyer M, Thiele C, Shalek AK, Feißt A, Thomas D, Dickten H, Beyer M, Baum P, Yosef N, Aschenbrenner AC, Ulas T, Hasenauer J, Theis FJ, Skowasch D, Schultze JL. Alveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation. Front Immunol 2022; 13:917232. [PMID: 35979364 PMCID: PMC9377018 DOI: 10.3389/fimmu.2022.917232] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/24/2022] [Indexed: 12/13/2022] Open
Abstract
Despite its high prevalence, the cellular and molecular mechanisms of chronic obstructive pulmonary disease (COPD) are far from being understood. Here, we determine disease-related changes in cellular and molecular compositions within the alveolar space and peripheral blood of a cohort of COPD patients and controls. Myeloid cells were the largest cellular compartment in the alveolar space with invading monocytes and proliferating macrophages elevated in COPD. Modeling cell-to-cell communication, signaling pathway usage, and transcription factor binding predicts TGF-β1 to be a major upstream regulator of transcriptional changes in alveolar macrophages of COPD patients. Functionally, macrophages in COPD showed reduced antigen presentation capacity, accumulation of cholesteryl ester, reduced cellular chemotaxis, and mitochondrial dysfunction, reminiscent of impaired immune activation.
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Affiliation(s)
- Kevin Baßler
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Wataru Fujii
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Theodore S. Kapellos
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Erika Dudkin
- Computational Life Sciences, Life & Medical Sciences (LIMES) Institute, University of Bonn, Neuherberg, Germany
| | - Nico Reusch
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Ari Horne
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | | | - Malte D. Luecken
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - Collins Osei-Sarpong
- Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Stefanie Warnat-Herresthal
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Lorenzo Bonaguro
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Jonas Schulte-Schrepping
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Allon Wagner
- Department of electrical engineering and computer science, University of California, Berkeley, CA, United States
- Center for computational biology, University of California, Berkeley, CA, United States
| | - Patrick Günther
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Bonn, Germany
| | - Carmen Pizarro
- Department of Internal Medicine II, University Hospital Bonn, Section of Pneumology, Bonn, Germany
| | - Tina Schreiber
- Department of Internal Medicine II, University Hospital Bonn, Section of Pneumology, Bonn, Germany
| | - Rainer Knoll
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Bonn, Germany
- Prevention, Aging & Systems Immunology, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Lisa Holsten
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Charlotte Kröger
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Prevention, Aging & Systems Immunology, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Elena De Domenico
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Matthias Becker
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Kristian Händler
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | | | | | - Heidi Theis
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Michael Kraut
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Marc H. Wadsworth
- Institute for Medical Engineering & Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Broad Institute of MIT and Harvard; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States
| | - Travis K. Hughes
- Institute of Structural Biology, University Hospital, University of Bonn, Bonn, Germany
| | - Humberto J. Ferreira
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Bonn, Germany
| | - Emily Hinkley
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Ines H. Kaltheuner
- Institute of Structural Biology, University Hospital, University of Bonn, Bonn, Germany
| | - Matthias Geyer
- Biochemistry & Cell Biology of Lipids, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Christoph Thiele
- University Clinics for Radiology, University Hospital Bonn, Bonn, Germany
| | - Alex K. Shalek
- Institute for Medical Engineering & Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Broad Institute of MIT and Harvard; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States
| | - Andreas Feißt
- University Clinics for Radiology, University Hospital Bonn, Bonn, Germany
| | - Daniel Thomas
- University Clinics for Radiology, University Hospital Bonn, Bonn, Germany
| | | | - Marc Beyer
- Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Patrick Baum
- Translational Medicine & Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Nir Yosef
- Department of electrical engineering and computer science, University of California, Berkeley, CA, United States
- Center for computational biology, University of California, Berkeley, CA, United States
- Chan-Zuckerberg Biohub, San Francisco, CA, United States
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Anna C. Aschenbrenner
- Prevention, Aging & Systems Immunology, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
| | - Thomas Ulas
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Jan Hasenauer
- Computational Life Sciences, Life & Medical Sciences (LIMES) Institute, University of Bonn, Neuherberg, Germany
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - Fabian J. Theis
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany, Department of Mathematics, Technical University of Munich, Munich, Germany
| | - Dirk Skowasch
- Department of Internal Medicine II, University Hospital Bonn, Section of Pneumology, Bonn, Germany
| | - Joachim L. Schultze
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
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10
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Frishberg A, Kooistra E, Nuesch-Germano M, Pecht T, Milman N, Reusch N, Warnat-Herresthal S, Bruse N, Händler K, Theis H, Kraut M, van Rijssen E, van Cranenbroek B, Koenen HJ, Heesakkers H, van den Boogaard M, Zegers M, Pickkers P, Becker M, Aschenbrenner AC, Ulas T, Theis FJ, Shen-Orr SS, Schultze JL, Kox M. Mature neutrophils and a NF-κB-to-IFN transition determine the unifying disease recovery dynamics in COVID-19. Cell Rep Med 2022; 3:100652. [PMID: 35675822 PMCID: PMC9110324 DOI: 10.1016/j.xcrm.2022.100652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/14/2022] [Accepted: 05/11/2022] [Indexed: 01/19/2023]
Abstract
Disease recovery dynamics are often difficult to assess, as patients display heterogeneous recovery courses. To model recovery dynamics, exemplified by severe COVID-19, we apply a computational scheme on longitudinally sampled blood transcriptomes, generating recovery states, which we then link to cellular and molecular mechanisms, presenting a framework for studying the kinetics of recovery compared with non-recovery over time and long-term effects of the disease. Specifically, a decrease in mature neutrophils is the strongest cellular effect during recovery, with direct implications on disease outcome. Furthermore, we present strong indications for global regulatory changes in gene programs, decoupled from cell compositional changes, including an early rise in T cell activation and differentiation, resulting in immune rebalancing between interferon and NF-κB activity and restoration of cell homeostasis. Overall, we present a clinically relevant computational framework for modeling disease recovery, paving the way for future studies of the recovery dynamics in other diseases and tissues.
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Affiliation(s)
- Amit Frishberg
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany; Institute of Computational Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Emma Kooistra
- Department of Intensive Care Medicine, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Melanie Nuesch-Germano
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Tal Pecht
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Neta Milman
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Nico Reusch
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Stefanie Warnat-Herresthal
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Niklas Bruse
- Department of Intensive Care Medicine, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Kristian Händler
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, Bonn, Germany
| | - Heidi Theis
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, Bonn, Germany
| | - Michael Kraut
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, Bonn, Germany
| | - Esther van Rijssen
- Laboratory for Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Bram van Cranenbroek
- Laboratory for Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hans Jpm Koenen
- Laboratory for Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hidde Heesakkers
- Department of Intensive Care Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Mark van den Boogaard
- Department of Intensive Care Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marieke Zegers
- Department of Intensive Care Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Peter Pickkers
- Department of Intensive Care Medicine, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Matthias Becker
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, Bonn, Germany
| | - Anna C Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands; Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, Bonn, Germany
| | - Thomas Ulas
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, Bonn, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Department of Mathematics, Technical University of Munich, 85748 Garching, Germany; Technical University of Munich, TUM School of Life Sciences Weihenstephan, 85354 Freising, Germany
| | - Shai S Shen-Orr
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, Bonn, Germany.
| | - Matthijs Kox
- Department of Intensive Care Medicine, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
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11
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Piazzesi A, Wang Y, Jackson J, Wischhof L, Zeisler-Diehl V, Scifo E, Oganezova I, Hoffmann T, Gómez Martín P, Bertan F, Wrobel CJJ, Schroeder FC, Ehninger D, Händler K, Schultze JL, Schreiber L, van Echten-Deckert G, Nicotera P, Bano D. CEST-2.2 overexpression alters lipid metabolism and extends longevity of mitochondrial mutants. EMBO Rep 2022; 23:e52606. [PMID: 35297148 PMCID: PMC9066074 DOI: 10.15252/embr.202152606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/14/2022] [Accepted: 02/22/2022] [Indexed: 12/17/2022] Open
Abstract
Mitochondrial dysfunction can either extend or decrease Caenorhabditis elegans lifespan, depending on whether transcriptionally regulated responses can elicit durable stress adaptation to otherwise detrimental lesions. Here, we test the hypothesis that enhanced metabolic flexibility is sufficient to circumvent bioenergetic abnormalities associated with the phenotypic threshold effect, thereby transforming short‐lived mitochondrial mutants into long‐lived ones. We find that CEST‐2.2, a carboxylesterase mainly localizes in the intestine, may stimulate the survival of mitochondrial deficient animals. We report that genetic manipulation of cest‐2.2 expression has a minor lifespan impact on wild‐type nematodes, whereas its overexpression markedly extends the lifespan of complex I‐deficient gas‐1(fc21) mutants. We profile the transcriptome and lipidome of cest‐2.2 overexpressing animals and show that CEST‐2.2 stimulates lipid metabolism and fatty acid beta‐oxidation, thereby enhancing mitochondrial respiratory capacity through complex II and LET‐721/ETFDH, despite the inherited genetic lesion of complex I. Together, our findings unveil a metabolic pathway that, through the tissue‐specific mobilization of lipid deposits, may influence the longevity of mitochondrial mutant C. elegans.
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Affiliation(s)
- Antonia Piazzesi
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Yiru Wang
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Joshua Jackson
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Lena Wischhof
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Enzo Scifo
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Ina Oganezova
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Thorben Hoffmann
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Fabio Bertan
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Chester J J Wrobel
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Dan Ehninger
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Kristian Händler
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany.,Department for Genomics and Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany
| | - Lukas Schreiber
- Institute of Cellular and Molecular Botany (IZMB), University of Bonn, Bonn, Germany
| | | | | | - Daniele Bano
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
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12
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Jackson J, Wischhof L, Scifo E, Pellizzer A, Wang Y, Piazzesi A, Gentile D, Siddig S, Stork M, Hopkins CE, Händler K, Weis J, Roos A, Schultze JL, Nicotera P, Ehninger D, Bano D. SGPL1 stimulates VPS39 recruitment to the mitochondria in MICU1 deficient cells. Mol Metab 2022; 61:101503. [PMID: 35452878 PMCID: PMC9170783 DOI: 10.1016/j.molmet.2022.101503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/08/2022] [Accepted: 04/15/2022] [Indexed: 01/21/2023] Open
Abstract
Objective Mitochondrial “retrograde” signaling may stimulate organelle biogenesis as a compensatory adaptation to aberrant activity of the oxidative phosphorylation (OXPHOS) system. To maintain energy-consuming processes in OXPHOS deficient cells, alternative metabolic pathways are functionally coupled to the degradation, recycling and redistribution of biomolecules across distinct intracellular compartments. While transcriptional regulation of mitochondrial network expansion has been the focus of many studies, the molecular mechanisms promoting mitochondrial maintenance in energy-deprived cells remain poorly investigated. Methods We performed transcriptomics, quantitative proteomics and lifespan assays to identify pathways that are mechanistically linked to mitochondrial network expansion and homeostasis in Caenorhabditis elegans lacking the mitochondrial calcium uptake protein 1 (MICU-1/MICU1). To support our findings, we carried out biochemical and image analyses in mammalian cells and mouse-derived tissues. Results We report that micu-1(null) mutations impair the OXPHOS system and promote C. elegans longevity through a transcriptional program that is independent of the mitochondrial calcium uniporter MCU-1/MCU and the essential MCU regulator EMRE-1/EMRE. We identify sphingosine phosphate lyase SPL-1/SGPL1 and the ATFS-1-target HOPS complex subunit VPS-39/VPS39 as critical lifespan modulators of micu-1(null) mutant animals. Cross-species investigation indicates that SGPL1 upregulation stimulates VPS39 recruitment to the mitochondria, thereby enhancing mitochondria-lysosome contacts. Consistently, VPS39 downregulation compromises mitochondrial network maintenance and basal autophagic flux in MICU1 deficient cells. In mouse-derived muscles, we show that VPS39 recruitment to the mitochondria may represent a common signature associated with altered OXPHOS system. Conclusions Our findings reveal a previously unrecognized SGPL1/VPS39 axis that stimulates intracellular organelle interactions and sustains autophagy and mitochondrial homeostasis in OXPHOS deficient cells. micu-1(null) nematodes are long-lived mitochondrial mutants. MICU-1/MICU1 deficiency stimulates VPS-39/VPS39 and SPL-1/SGPL1 upregulation. VPS-39 sustains mitochondrial network expansion in micu-1(null) nematodes. VPS39 and SGPL1 expression influences mitochondria-lysosome contact sites in MICU1 deficient cells. VPS39/SGPL1 signaling may be a common signature of mitochondrial deficient cells.
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Affiliation(s)
- Joshua Jackson
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Lena Wischhof
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Enzo Scifo
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Anna Pellizzer
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Yiru Wang
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Antonia Piazzesi
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Debora Gentile
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Sana Siddig
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Miriam Stork
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Kristian Händler
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany; PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany
| | - Joachim Weis
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Andreas Roos
- Universitätsklinikum Essen and Universität Duisburg-Essen, Essen, Germany
| | - Joachim L Schultze
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany; PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany; LIMES Institute, Department for Genomics and Immunoregulation, University of Bonn, Bonn, Germany
| | | | - Dan Ehninger
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Daniele Bano
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
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13
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Duy PQ, Weise SC, Marini C, Li XJ, Liang D, Dahl PJ, Ma S, Spajic A, Dong W, Juusola J, Kiziltug E, Kundishora AJ, Koundal S, Pedram MZ, Torres-Fernández LA, Händler K, De Domenico E, Becker M, Ulas T, Juranek SA, Cuevas E, Hao LT, Jux B, Sousa AMM, Liu F, Kim SK, Li M, Yang Y, Takeo Y, Duque A, Nelson-Williams C, Ha Y, Selvaganesan K, Robert SM, Singh AK, Allington G, Furey CG, Timberlake AT, Reeves BC, Smith H, Dunbar A, DeSpenza T, Goto J, Marlier A, Moreno-De-Luca A, Yu X, Butler WE, Carter BS, Lake EMR, Constable RT, Rakic P, Lin H, Deniz E, Benveniste H, Malvankar NS, Estrada-Veras JI, Walsh CA, Alper SL, Schultze JL, Paeschke K, Doetzlhofer A, Wulczyn FG, Jin SC, Lifton RP, Sestan N, Kolanus W, Kahle KT. Impaired neurogenesis alters brain biomechanics in a neuroprogenitor-based genetic subtype of congenital hydrocephalus. Nat Neurosci 2022; 25:458-473. [PMID: 35379995 PMCID: PMC9664907 DOI: 10.1038/s41593-022-01043-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/28/2022] [Indexed: 01/16/2023]
Abstract
Hydrocephalus, characterized by cerebral ventricular dilatation, is routinely attributed to primary defects in cerebrospinal fluid (CSF) homeostasis. This fosters CSF shunting as the leading reason for brain surgery in children despite considerable disease heterogeneity. In this study, by integrating human brain transcriptomics with whole-exome sequencing of 483 patients with congenital hydrocephalus (CH), we found convergence of CH risk genes in embryonic neuroepithelial stem cells. Of all CH risk genes, TRIM71/lin-41 harbors the most de novo mutations and is most specifically expressed in neuroepithelial cells. Mice harboring neuroepithelial cell-specific Trim71 deletion or CH-specific Trim71 mutation exhibit prenatal hydrocephalus. CH mutations disrupt TRIM71 binding to its RNA targets, causing premature neuroepithelial cell differentiation and reduced neurogenesis. Cortical hypoplasia leads to a hypercompliant cortex and secondary ventricular enlargement without primary defects in CSF circulation. These data highlight the importance of precisely regulated neuroepithelial cell fate for normal brain-CSF biomechanics and support a clinically relevant neuroprogenitor-based paradigm of CH.
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Affiliation(s)
- Phan Q Duy
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA.,Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA.,Medical Scientist Training Program, Yale University School of Medicine, New Haven, CT, USA
| | - Stefan C Weise
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Claudia Marini
- Institute for Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Xiao-Jun Li
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Center for Hearing and Balance, Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dan Liang
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Peter J Dahl
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Shaojie Ma
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Ana Spajic
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Weilai Dong
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | | | - Emre Kiziltug
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Adam J Kundishora
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Sunil Koundal
- Department of Anesthesiology, Yale University School of Medicine, New Haven, CT, USA
| | - Maysam Z Pedram
- Department of Anesthesiology, Yale University School of Medicine, New Haven, CT, USA
| | - Lucia A Torres-Fernández
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Kristian Händler
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE). PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, Bonn, Germany
| | - Elena De Domenico
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE). PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, Bonn, Germany
| | - Matthias Becker
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE). PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, Bonn, Germany
| | - Thomas Ulas
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE). PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, Bonn, Germany
| | - Stefan A Juranek
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Elisa Cuevas
- Stem Cells and Regenerative Medicine Section, University College London Great Ormond Street Institute of Child Health, London, UK
| | - Le Thi Hao
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Bettina Jux
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - André M M Sousa
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Fuchen Liu
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Suel-Kee Kim
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Mingfeng Li
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Yiying Yang
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Yutaka Takeo
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Alvaro Duque
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | | | - Yonghyun Ha
- Department of Radiology and Biomedical Imaging, Yale University School of Medicine, New Haven, CT, USA
| | - Kartiga Selvaganesan
- Department of Radiology and Biomedical Imaging, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie M Robert
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Amrita K Singh
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Garrett Allington
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Charuta G Furey
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew T Timberlake
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Benjamin C Reeves
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Hannah Smith
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Ashley Dunbar
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Tyrone DeSpenza
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - June Goto
- Division of Pediatric Neurosurgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Arnaud Marlier
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Andres Moreno-De-Luca
- Department of Radiology, Autism & Developmental Medicine Institute, Genomic Medicine Institute, Geisinger, Danville, PA, USA
| | - Xin Yu
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - William E Butler
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Evelyn M R Lake
- Department of Radiology and Biomedical Imaging, Yale University School of Medicine, New Haven, CT, USA
| | - R Todd Constable
- Department of Radiology and Biomedical Imaging, Yale University School of Medicine, New Haven, CT, USA
| | - Pasko Rakic
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Haifan Lin
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Engin Deniz
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Helene Benveniste
- Department of Anesthesiology, Yale University School of Medicine, New Haven, CT, USA
| | - Nikhil S Malvankar
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Juvianee I Estrada-Veras
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.,Pediatric Subspecialty Genetics Walter Reed National Military Medical Center, Bethesda, MD, USA.,Murtha Cancer Center/Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.,Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Seth L Alper
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Nephrology and Vascular Biology Research Center, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE). PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Angelika Doetzlhofer
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Center for Hearing and Balance, Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - F Gregory Wulczyn
- Institute for Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Waldemar Kolanus
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. .,Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Harvard Center for Hydrocephalus and Neurodevelopmental Disorders, Massachusetts General Hospital, Boston, MA, USA.
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14
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Pozojevic J, Algodon SM, Cruz JN, Trinh J, Brüggemann N, Laß J, Grütz K, Schaake S, Tse R, Yumiceba V, Kruse N, Schulz K, Sreenivasan VKA, Rosales RL, Jamora RDG, Diesta CCE, Matschke J, Glatzel M, Seibler P, Händler K, Rakovic A, Kirchner H, Spielmann M, Kaiser FJ, Klein C, Westenberger A. Transcriptional Alterations in X-Linked Dystonia–Parkinsonism Caused by the SVA Retrotransposon. Int J Mol Sci 2022; 23:ijms23042231. [PMID: 35216353 PMCID: PMC8875906 DOI: 10.3390/ijms23042231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 02/05/2023] Open
Abstract
X-linked dystonia–parkinsonism (XDP) is a severe neurodegenerative disorder that manifests as adult-onset dystonia combined with parkinsonism. A SINE-VNTR-Alu (SVA) retrotransposon inserted in an intron of the TAF1 gene reduces its expression and alters splicing in XDP patient-derived cells. As a consequence, increased levels of the TAF1 intron retention transcript TAF1-32i can be found in XDP cells as compared to healthy controls. Here, we investigate the sequence of the deep intronic region included in this transcript and show that it is also present in cells from healthy individuals, albeit in lower amounts than in XDP cells, and that it undergoes degradation by nonsense-mediated mRNA decay. Furthermore, we investigate epigenetic marks (e.g., DNA methylation and histone modifications) present in this intronic region and the spanning sequence. Finally, we show that the SVA evinces regulatory potential, as demonstrated by its ability to repress the TAF1 promoter in vitro. Our results enable a better understanding of the disease mechanisms underlying XDP and transcriptional alterations caused by SVA retrotransposons.
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Affiliation(s)
- Jelena Pozojevic
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Shela Marie Algodon
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Joseph Neos Cruz
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Norbert Brüggemann
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
- Department of Neurology, University Hospital Schleswig Holstein, 23538 Lübeck, Germany
| | - Joshua Laß
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Karen Grütz
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Susen Schaake
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Ronnie Tse
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Veronica Yumiceba
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Nathalie Kruse
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Kristin Schulz
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Varun K. A. Sreenivasan
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Raymond L. Rosales
- The Hospital Neuroscience Institute, Department of Neurology and Psychiatry and The FMS-Research Center for Health Sciences, University of Santo Tomas, Manila 1008, Philippines;
| | - Roland Dominic G. Jamora
- Department of Neurosciences, College of Medicine-Philippine General Hospital, University of the Philippines Manila, Manila 1000, Philippines;
| | - Cid Czarina E. Diesta
- Department of Neurosciences, Movement Disorders Clinic, Makati Medical Center, Makati City 1229, Philippines;
| | - Jakob Matschke
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (J.M.); (M.G.)
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (J.M.); (M.G.)
| | - Philip Seibler
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Kristian Händler
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Aleksandar Rakovic
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Henriette Kirchner
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Malte Spielmann
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Lübeck/Kiel, 23538 Lübeck, Germany
| | - Frank J. Kaiser
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45147 Essen, Germany;
- Essener Zentrum für Seltene Erkrankungen, Universitätsmedizin Essen, 45147 Essen, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
- Correspondence: (C.K.); (A.W.)
| | - Ana Westenberger
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
- Correspondence: (C.K.); (A.W.)
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15
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Gerber JP, Russ J, Chandrasekar V, Offermann N, Lee HM, Spear S, Guzzi N, Maida S, Pattabiraman S, Zhang R, Kayvanjoo AH, Datta P, Kasturiarachchi J, Sposito T, Izotova N, Händler K, Adams PD, Marafioti T, Enver T, Wenzel J, Beyer M, Mass E, Bellodi C, Schultze JL, Capasso M, Nimmo R, Salomoni P. Author Correction: Aberrant chromatin landscape following loss of the H3.3 chaperone Daxx in haematopoietic precursors leads to Pu.1-mediated neutrophilia and inflammation. Nat Cell Biol 2022; 24:123. [PMID: 34983954 PMCID: PMC9119264 DOI: 10.1038/s41556-021-00833-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Julia P Gerber
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Cancer Biology, UCL Cancer Institute, London, UK
| | - Jenny Russ
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Nina Offermann
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Hang-Mao Lee
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Sarah Spear
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Nicola Guzzi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Simona Maida
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Ruoyu Zhang
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Amir H Kayvanjoo
- Life and Medical Sciences (LIMES) Institute, Developmental Biology of the Immune System, University of Bonn, Bonn, Germany
| | - Preeta Datta
- Department of Cancer Biology, UCL Cancer Institute, London, UK
| | | | - Teresa Sposito
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Natalia Izotova
- Department of Cancer Biology, UCL Cancer Institute, London, UK
| | - Kristian Händler
- Platform for Single Cell Genomics and Epigenomics (PRECISE) at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, USA
| | - Teresa Marafioti
- Department of Cancer Biology, UCL Cancer Institute, London, UK.,Department of Pathology, University College London, London, UK
| | - Tariq Enver
- Department of Cancer Biology, UCL Cancer Institute, London, UK
| | - Jörg Wenzel
- Department of Dermatology and Allergy, University Medical Center, Bonn, Germany
| | - Marc Beyer
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Platform for Single Cell Genomics and Epigenomics (PRECISE) at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Elvira Mass
- Life and Medical Sciences (LIMES) Institute, Developmental Biology of the Immune System, University of Bonn, Bonn, Germany
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Joachim L Schultze
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Platform for Single Cell Genomics and Epigenomics (PRECISE) at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany.,Genomics and Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany
| | - Melania Capasso
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Rachael Nimmo
- Department of Cancer Biology, UCL Cancer Institute, London, UK
| | - Paolo Salomoni
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany. .,Department of Cancer Biology, UCL Cancer Institute, London, UK.
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16
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Kummer MP, Ising C, Kummer C, Sarlus H, Griep A, Vieira-Saecker A, Schwartz S, Halle A, Brückner M, Händler K, Schultze JL, Beyer M, Latz E, Heneka MT. Microglial PD-1 stimulation by astrocytic PD-L1 suppresses neuroinflammation and Alzheimer's disease pathology. EMBO J 2021; 40:e108662. [PMID: 34825707 PMCID: PMC8672180 DOI: 10.15252/embj.2021108662] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/27/2021] [Accepted: 10/25/2021] [Indexed: 12/14/2022] Open
Abstract
Chronic neuroinflammation is a pathogenic component of Alzheimer’s disease (AD) that may limit the ability of the brain to clear amyloid deposits and cellular debris. Tight control of the immune system is therefore key to sustain the ability of the brain to repair itself during homeostasis and disease. The immune‐cell checkpoint receptor/ligand pair PD‐1/PD‐L1, known for their inhibitory immune function, is expressed also in the brain. Here, we report upregulated expression of PD‐L1 and PD‐1 in astrocytes and microglia, respectively, surrounding amyloid plaques in AD patients and in the APP/PS1 AD mouse model. We observed juxtamembrane shedding of PD‐L1 from astrocytes, which may mediate ectodomain signaling to PD‐1‐expressing microglia. Deletion of microglial PD‐1 evoked an inflammatory response and compromised amyloid‐β peptide (Aβ) uptake. APP/PS1 mice deficient for PD‐1 exhibited increased deposition of Aβ, reduced microglial Aβ uptake, and decreased expression of the Aβ receptor CD36 on microglia. Therefore, ineffective immune regulation by the PD‐1/PD‐L1 axis contributes to Aβ plaque deposition during chronic neuroinflammation in AD.
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Affiliation(s)
- Markus P Kummer
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn Medical Faculty, Bonn, Germany
| | - Christina Ising
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn Medical Faculty, Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Christiane Kummer
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn Medical Faculty, Bonn, Germany
| | - Heela Sarlus
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Angelika Griep
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Ana Vieira-Saecker
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn Medical Faculty, Bonn, Germany
| | - Stephanie Schwartz
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn Medical Faculty, Bonn, Germany
| | - Annett Halle
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Kristian Händler
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and University of Bonn, Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Marc Beyer
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and University of Bonn, Bonn, Germany.,Molecular Immunology in Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Eicke Latz
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Institute of Innate Immunity, University of Bonn, Bonn, Germany.,Department of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Michael T Heneka
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn Medical Faculty, Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA, USA
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17
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Fujii W, Kapellos TS, Baßler K, Händler K, Holsten L, Knoll R, Warnat-Herresthal S, Oestreich M, Hinkley ER, Hasenauer J, Pizarro C, Thiele C, Aschenbrenner AC, Ulas T, Skowasch D, Schultze JL. Alveolar macrophage transcriptomic profiling in COPD shows major lipid metabolism changes. ERJ Open Res 2021; 7:00915-2020. [PMID: 34527724 PMCID: PMC8435801 DOI: 10.1183/23120541.00915-2020] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 04/24/2021] [Indexed: 01/14/2023] Open
Abstract
Background Immune cells play a major role in the pathogenesis of COPD. Changes in the distribution and cellular functions of major immune cells, such as alveolar macrophages (AMs) and neutrophils are well known; however, their transcriptional reprogramming and contribution to the pathophysiology of COPD are still not fully understood. Method To determine changes in transcriptional reprogramming and lipid metabolism in the major immune cell type within bronchoalveolar lavage fluid, we analysed whole transcriptomes and lipidomes of sorted CD45+Lin−HLA-DR+CD66b−Autofluorescencehi AMs from controls and COPD patients. Results We observed global transcriptional reprogramming featuring a spectrum of activation states, including pro- and anti-inflammatory signatures. We further detected significant changes between COPD patients and controls in genes involved in lipid metabolism, such as fatty acid biosynthesis in GOLD2 patients. Based on these findings, assessment of a total of 202 lipid species in sorted AMs revealed changes of cholesteryl esters, monoacylglycerols and phospholipids in a disease grade-dependent manner. Conclusions Transcriptome and lipidome profiling of COPD AMs revealed GOLD grade-dependent changes, such as in cholesterol metabolism and interferon-α and γ responses. AMs from COPD patients undergo GOLD grade-specific transcriptional reprogramming and acquire a complex activation profile. Among the observed changes are gene programmes involved in lipid metabolism that translate into alterations in the AM lipidome.https://bit.ly/3sYAqgd
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Affiliation(s)
- Wataru Fujii
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Co-first authors
| | - Theodore S Kapellos
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Co-first authors
| | - Kevin Baßler
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Co-first authors
| | - Kristian Händler
- Platform for Single Cell Genomics and Epigenomics (PRECISE), German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Lisa Holsten
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Rainer Knoll
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Stefanie Warnat-Herresthal
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Marie Oestreich
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Emily R Hinkley
- Platform for Single Cell Genomics and Epigenomics (PRECISE), German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Jan Hasenauer
- Interdisciplinary Research Unit Mathematics and Life Sciences, Dept of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
| | - Carmen Pizarro
- Dept of Internal Medicine II, University Hospital Bonn, Section of Pneumology, Bonn, Germany
| | - Christoph Thiele
- Membrane Biochemistry, LIMES Institute, University of Bonn, Bonn, Germany
| | - Anna C Aschenbrenner
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Dept of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thomas Ulas
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Dirk Skowasch
- Dept of Internal Medicine II, University Hospital Bonn, Section of Pneumology, Bonn, Germany.,Co-senior authors
| | - Joachim L Schultze
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Platform for Single Cell Genomics and Epigenomics (PRECISE), German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany.,Co-senior authors
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18
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Zocher S, Overall RW, Berdugo-Vega G, Rund N, Karasinsky A, Adusumilli VS, Steinhauer C, Scheibenstock S, Händler K, Schultze JL, Calegari F, Kempermann G. De novo DNA methylation controls neuronal maturation during adult hippocampal neurogenesis. EMBO J 2021; 40:e107100. [PMID: 34337766 PMCID: PMC8441477 DOI: 10.15252/embj.2020107100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 06/28/2021] [Accepted: 07/02/2021] [Indexed: 11/20/2022] Open
Abstract
Adult neurogenesis enables the life‐long addition of functional neurons to the hippocampus and is regulated by both cell‐intrinsic molecular programs and behavioral activity. De novo DNA methylation is crucial for embryonic brain development, but its role during adult hippocampal neurogenesis has remained unknown. Here, we show that de novo DNA methylation is critical for maturation and functional integration of adult‐born neurons in the mouse hippocampus. Bisulfite sequencing revealed that de novo DNA methyltransferases target neuronal enhancers and gene bodies during adult hippocampal neural stem cell differentiation, to establish neuronal methylomes and facilitate transcriptional up‐regulation of neuronal genes. Inducible deletion of both de novo DNA methyltransferases Dnmt3a and Dnmt3b in adult neural stem cells did not affect proliferation or fate specification, but specifically impaired dendritic outgrowth and synaptogenesis of newborn neurons, thereby hampering their functional maturation. Consequently, abolishing de novo DNA methylation modulated activation patterns in the hippocampal circuitry and caused specific deficits in hippocampus‐dependent learning and memory. Our results demonstrate that proper establishment of neuronal methylomes during adult neurogenesis is fundamental for hippocampal function.
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Affiliation(s)
- Sara Zocher
- German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Rupert W Overall
- German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Gabriel Berdugo-Vega
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Nicole Rund
- German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Anne Karasinsky
- German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Vijay S Adusumilli
- German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Christina Steinhauer
- German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Sina Scheibenstock
- German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Kristian Händler
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases, University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases, University of Bonn, Bonn, Germany
| | - Federico Calegari
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Gerd Kempermann
- German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
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19
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Beckert V, Rassmann S, Kayvanjoo AH, Klausen C, Bonaguro L, Botermann DS, Krause M, Moreth K, Spielmann N, da Silva-Buttkus P, Fuchs H, Gailus-Durner V, de Angelis MH, Händler K, Ulas T, Aschenbrenner AC, Mass E, Wachten D. Creld1 regulates myocardial development and function. J Mol Cell Cardiol 2021; 156:45-56. [PMID: 33773996 DOI: 10.1016/j.yjmcc.2021.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/25/2021] [Accepted: 03/18/2021] [Indexed: 12/14/2022]
Abstract
CRELD1 (Cysteine-Rich with EGF-Like Domains 1) is a risk gene for non-syndromic atrioventricular septal defects in human patients. In a mouse model, Creld1 has been shown to be essential for heart development, particularly in septum and valve formation. However, due to the embryonic lethality of global Creld1 knockout (KO) mice, its cell type-specific function during peri- and postnatal stages remains unknown. Here, we generated conditional Creld1 KO mice lacking Creld1 either in the endocardium (KOTie2) or the myocardium (KOMyHC). Using a combination of cardiac phenotyping, histology, immunohistochemistry, RNA-sequencing, and flow cytometry, we demonstrate that Creld1 function in the endocardium is dispensable for heart development. Lack of myocardial Creld1 causes extracellular matrix remodeling and trabeculation defects by modulation of the Notch1 signaling pathway. Hence, KOMyHC mice die early postnatally due to myocardial hypoplasia. Our results reveal that Creld1 not only controls the formation of septa and valves at an early stage during heart development, but also cardiac maturation and function at a later stage. These findings underline the central role of Creld1 in mammalian heart development and function.
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Affiliation(s)
- Vera Beckert
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Sebastian Rassmann
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Amir Hossein Kayvanjoo
- Life & Medical Institute (LIMES), Developmental Biology of the Immune System, University of Bonn, 53115 Bonn, Germany
| | - Christina Klausen
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Lorenzo Bonaguro
- Life & Medical Institute (LIMES), Genomics and Immunoregulation, University of Bonn, 53115 Bonn, Germany
| | - Dominik Simon Botermann
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Melanie Krause
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Kristin Moreth
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Nadine Spielmann
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Patricia da Silva-Buttkus
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Chair of Experimental Genetics, School of Life Science Weihenstephan, Technical University Munich, 85354 Freising, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Kristian Händler
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Single Cell Genomics and Epigenomics at the DZNE and the University of Bonn, 53127 Bonn, Germany
| | - Thomas Ulas
- Life & Medical Institute (LIMES), Genomics and Immunoregulation, University of Bonn, 53115 Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Single Cell Genomics and Epigenomics at the DZNE and the University of Bonn, 53127 Bonn, Germany
| | - Anna C Aschenbrenner
- Life & Medical Institute (LIMES), Genomics and Immunoregulation, University of Bonn, 53115 Bonn, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Elvira Mass
- Life & Medical Institute (LIMES), Developmental Biology of the Immune System, University of Bonn, 53115 Bonn, Germany.
| | - Dagmar Wachten
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, 53127 Bonn, Germany.
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20
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Warnat-Herresthal S, Schultze H, Shastry KL, Manamohan S, Mukherjee S, Garg V, Sarveswara R, Händler K, Pickkers P, Aziz NA, Ktena S, Tran F, Bitzer M, Ossowski S, Casadei N, Herr C, Petersheim D, Behrends U, Kern F, Fehlmann T, Schommers P, Lehmann C, Augustin M, Rybniker J, Altmüller J, Mishra N, Bernardes JP, Krämer B, Bonaguro L, Schulte-Schrepping J, De Domenico E, Siever C, Kraut M, Desai M, Monnet B, Saridaki M, Siegel CM, Drews A, Nuesch-Germano M, Theis H, Heyckendorf J, Schreiber S, Kim-Hellmuth S, Nattermann J, Skowasch D, Kurth I, Keller A, Bals R, Nürnberg P, Rieß O, Rosenstiel P, Netea MG, Theis F, Mukherjee S, Backes M, Aschenbrenner AC, Ulas T, Breteler MMB, Giamarellos-Bourboulis EJ, Kox M, Becker M, Cheran S, Woodacre MS, Goh EL, Schultze JL. Swarm Learning for decentralized and confidential clinical machine learning. Nature 2021; 594:265-270. [PMID: 34040261 PMCID: PMC8189907 DOI: 10.1038/s41586-021-03583-3] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 04/26/2021] [Indexed: 01/08/2023]
Abstract
Fast and reliable detection of patients with severe and heterogeneous illnesses is a major goal of precision medicine1,2. Patients with leukaemia can be identified using machine learning on the basis of their blood transcriptomes3. However, there is an increasing divide between what is technically possible and what is allowed, because of privacy legislation4,5. Here, to facilitate the integration of any medical data from any data owner worldwide without violating privacy laws, we introduce Swarm Learning—a decentralized machine-learning approach that unites edge computing, blockchain-based peer-to-peer networking and coordination while maintaining confidentiality without the need for a central coordinator, thereby going beyond federated learning. To illustrate the feasibility of using Swarm Learning to develop disease classifiers using distributed data, we chose four use cases of heterogeneous diseases (COVID-19, tuberculosis, leukaemia and lung pathologies). With more than 16,400 blood transcriptomes derived from 127 clinical studies with non-uniform distributions of cases and controls and substantial study biases, as well as more than 95,000 chest X-ray images, we show that Swarm Learning classifiers outperform those developed at individual sites. In addition, Swarm Learning completely fulfils local confidentiality regulations by design. We believe that this approach will notably accelerate the introduction of precision medicine. Swarm Learning is a decentralized machine learning approach that outperforms classifiers developed at individual sites for COVID-19 and other diseases while preserving confidentiality and privacy.
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Affiliation(s)
- Stefanie Warnat-Herresthal
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | | | | | | | | | - Vishesh Garg
- Hewlett Packard Enterprise, Houston, TX, USA.,Mesh Dynamics, Bangalore, India
| | | | - Kristian Händler
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany
| | - Peter Pickkers
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - N Ahmad Aziz
- Population Health Sciences, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Department of Neurology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Sofia Ktena
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Florian Tran
- Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany.,Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Michael Bitzer
- Department of Internal Medicine I, University Hospital, University of Tübingen, Tübingen, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,NGS Competence Center Tübingen, Tübingen, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,NGS Competence Center Tübingen, Tübingen, Germany
| | - Christian Herr
- Department of Internal Medicine V, Saarland University Hospital, Homburg, Germany
| | - Daniel Petersheim
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital LMU Munich, Munich, Germany
| | - Uta Behrends
- Children's Hospital, Medical Faculty, Technical University Munich, Munich, Germany
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Tobias Fehlmann
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Philipp Schommers
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Clara Lehmann
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Max Augustin
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Jan Rybniker
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, West German Genome Center, University of Cologne, Cologne, Germany
| | - Neha Mishra
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Joana P Bernardes
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Benjamin Krämer
- Clinical Infectious Diseases, Research Center Borstel and German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jonas Schulte-Schrepping
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Elena De Domenico
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany
| | | | - Michael Kraut
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany
| | | | | | - Maria Saridaki
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | | | - Anna Drews
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany
| | - Melanie Nuesch-Germano
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Heidi Theis
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany
| | - Jan Heyckendorf
- Clinical Infectious Diseases, Research Center Borstel and German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Stefan Schreiber
- Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Sarah Kim-Hellmuth
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital LMU Munich, Munich, Germany
| | | | - Jacob Nattermann
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Dirk Skowasch
- Department of Internal Medicine II - Cardiology/Pneumology, University of Bonn, Bonn, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert Bals
- Department of Internal Medicine V, Saarland University Hospital, Homburg, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, West German Genome Center, University of Cologne, Cologne, Germany
| | - Olaf Rieß
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,NGS Competence Center Tübingen, Tübingen, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands.,Immunology & Metabolism, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Center Munich (HMGU), Neuherberg, Germany
| | - Sach Mukherjee
- Statistics and Machine Learning, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Michael Backes
- CISPA Helmholtz Center for Information Security, Saarbrücken, Germany
| | - Anna C Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany.,Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thomas Ulas
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | | | - Monique M B Breteler
- Population Health Sciences, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
| | | | - Matthijs Kox
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Matthias Becker
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany
| | | | | | - Eng Lim Goh
- Hewlett Packard Enterprise, Houston, TX, USA
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany. .,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany. .,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany.
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21
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Torres Fernández LA, Mitschka S, Ulas T, Weise S, Dahm K, Becker M, Händler K, Beyer M, Windhausen J, Schultze JL, Kolanus W. The stem cell-specific protein TRIM71 inhibits maturation and activity of the pro-differentiation miRNA let-7 via two independent molecular mechanisms. RNA 2021; 27:rna.078696.121. [PMID: 33975917 PMCID: PMC8208056 DOI: 10.1261/rna.078696.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/29/2021] [Indexed: 05/05/2023]
Abstract
The stem cell-specific RNA-binding protein TRIM71/LIN-41 was the first identified target of the pro-differentiation and tumor suppressor miRNA let-7. TRIM71 has essential functions in embryonic development and a proposed oncogenic role in several cancer types, such as hepatocellular carcinoma. Here, we show that TRIM71 regulates let-7 expression and activity via two independent mechanisms. On the one hand, TRIM71 enhances pre-let-7 degradation through its direct interaction with LIN28 and TUT4, thereby inhibiting let-7 maturation and indirectly promoting the stabilization of let-7 targets. On the other hand, TRIM71 represses the activity of mature let-7 via its RNA-dependent interaction with the RNA-Induced Silencing Complex (RISC) effector protein AGO2. We found that TRIM71 directly binds and stabilizes let-7 targets, suggesting that let-7 activity inhibition occurs on active RISCs. MiRNA enrichment analysis of several transcriptomic datasets from mouse embryonic stem cells and human hepatocellular carcinoma cells suggests that these let-7 regulatory mechanisms shape transcriptomic changes during developmental and oncogenic processes. Altogether, our work reveals a novel role for TRIM71 as a miRNA repressor and sheds light on a dual mechanism of let-7 regulation.
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Affiliation(s)
| | | | - Thomas Ulas
- German Center for Neurodegenerative Diseases (DZNE) & Life and Medical Sciences Institute (LIMES), University of Bonn
| | - Stefan Weise
- Life and Medical Sciences Institute (LIMES), University of Bonn
| | - Kilian Dahm
- Life and Medical Sciences Institute (LIMES), University of Bonn
| | - Matthias Becker
- German Center for Neurodegenerative Diseases (DZNE), University of Bonn
| | - Kristian Händler
- German Center for Neurodegenerative Diseases (DZNE), University of Bonn
| | - Marc Beyer
- Life and Medical Sciences Institute (LIMES)
| | | | - Joachim L Schultze
- German Center for Neurodegenerative Diseases (DZNE) & Life and Medical Sciences Institute (LIMES), University of Bonn
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22
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Aschenbrenner AC, Mouktaroudi M, Krämer B, Oestreich M, Antonakos N, Nuesch-Germano M, Gkizeli K, Bonaguro L, Reusch N, Baßler K, Saridaki M, Knoll R, Pecht T, Kapellos TS, Doulou S, Kröger C, Herbert M, Holsten L, Horne A, Gemünd ID, Rovina N, Agrawal S, Dahm K, van Uelft M, Drews A, Lenkeit L, Bruse N, Gerretsen J, Gierlich J, Becker M, Händler K, Kraut M, Theis H, Mengiste S, De Domenico E, Schulte-Schrepping J, Seep L, Raabe J, Hoffmeister C, ToVinh M, Keitel V, Rieke G, Talevi V, Skowasch D, Aziz NA, Pickkers P, van de Veerdonk FL, Netea MG, Schultze JL, Kox M, Breteler MMB, Nattermann J, Koutsoukou A, Giamarellos-Bourboulis EJ, Ulas T. Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients. Genome Med 2021; 13:7. [PMID: 33441124 DOI: 10.1101/2020.07.07.20148395] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/18/2020] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 pandemic is currently leading to increasing numbers of COVID-19 patients all over the world. Clinical presentations range from asymptomatic, mild respiratory tract infection, to severe cases with acute respiratory distress syndrome, respiratory failure, and death. Reports on a dysregulated immune system in the severe cases call for a better characterization and understanding of the changes in the immune system. METHODS In order to dissect COVID-19-driven immune host responses, we performed RNA-seq of whole blood cell transcriptomes and granulocyte preparations from mild and severe COVID-19 patients and analyzed the data using a combination of conventional and data-driven co-expression analysis. Additionally, publicly available data was used to show the distinction from COVID-19 to other diseases. Reverse drug target prediction was used to identify known or novel drug candidates based on finding from data-driven findings. RESULTS Here, we profiled whole blood transcriptomes of 39 COVID-19 patients and 10 control donors enabling a data-driven stratification based on molecular phenotype. Neutrophil activation-associated signatures were prominently enriched in severe patient groups, which was corroborated in whole blood transcriptomes from an independent second cohort of 30 as well as in granulocyte samples from a third cohort of 16 COVID-19 patients (44 samples). Comparison of COVID-19 blood transcriptomes with those of a collection of over 3100 samples derived from 12 different viral infections, inflammatory diseases, and independent control samples revealed highly specific transcriptome signatures for COVID-19. Further, stratified transcriptomes predicted patient subgroup-specific drug candidates targeting the dysregulated systemic immune response of the host. CONCLUSIONS Our study provides novel insights in the distinct molecular subgroups or phenotypes that are not simply explained by clinical parameters. We show that whole blood transcriptomes are extremely informative for COVID-19 since they capture granulocytes which are major drivers of disease severity.
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Affiliation(s)
- Anna C Aschenbrenner
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maria Mouktaroudi
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Benjamin Krämer
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | - Marie Oestreich
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nikolaos Antonakos
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Melanie Nuesch-Germano
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Konstantina Gkizeli
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Lorenzo Bonaguro
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nico Reusch
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Kevin Baßler
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Maria Saridaki
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Rainer Knoll
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Tal Pecht
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Theodore S Kapellos
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Sarandia Doulou
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Charlotte Kröger
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Miriam Herbert
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Lisa Holsten
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Arik Horne
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Ioanna D Gemünd
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nikoletta Rovina
- 1st Department of Pulmonary Medicine and Intensive Care Unit, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Shobhit Agrawal
- West German Genome Center (WGGC), University of Bonn, Bonn, Germany
| | - Kilian Dahm
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Martina van Uelft
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Anna Drews
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Lena Lenkeit
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Niklas Bruse
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jelle Gerretsen
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jannik Gierlich
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Matthias Becker
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Kristian Händler
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Michael Kraut
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Heidi Theis
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Simachew Mengiste
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Elena De Domenico
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Jonas Schulte-Schrepping
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Lea Seep
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jan Raabe
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | | | - Michael ToVinh
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | - Verena Keitel
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Gereon Rieke
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | - Valentina Talevi
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Dirk Skowasch
- Department of Internal Medicine II, Section of Pneumology, University Hospital of Bonn (UKB), Bonn, Germany
| | - N Ahmad Aziz
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Peter Pickkers
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frank L van de Veerdonk
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Immunology & Metabolism, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Matthijs Kox
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Monique M B Breteler
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Jacob Nattermann
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
- German Center for Infection Research (DZIF), Bonn, Germany
| | - Antonia Koutsoukou
- 1st Department of Pulmonary Medicine and Intensive Care Unit, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | | | - Thomas Ulas
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany.
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23
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Aschenbrenner AC, Mouktaroudi M, Krämer B, Oestreich M, Antonakos N, Nuesch-Germano M, Gkizeli K, Bonaguro L, Reusch N, Baßler K, Saridaki M, Knoll R, Pecht T, Kapellos TS, Doulou S, Kröger C, Herbert M, Holsten L, Horne A, Gemünd ID, Rovina N, Agrawal S, Dahm K, van Uelft M, Drews A, Lenkeit L, Bruse N, Gerretsen J, Gierlich J, Becker M, Händler K, Kraut M, Theis H, Mengiste S, De Domenico E, Schulte-Schrepping J, Seep L, Raabe J, Hoffmeister C, ToVinh M, Keitel V, Rieke G, Talevi V, Skowasch D, Aziz NA, Pickkers P, van de Veerdonk FL, Netea MG, Schultze JL, Kox M, Breteler MMB, Nattermann J, Koutsoukou A, Giamarellos-Bourboulis EJ, Ulas T. Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients. Genome Med 2021; 13:7. [PMID: 33441124 PMCID: PMC7805430 DOI: 10.1186/s13073-020-00823-5] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/18/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 pandemic is currently leading to increasing numbers of COVID-19 patients all over the world. Clinical presentations range from asymptomatic, mild respiratory tract infection, to severe cases with acute respiratory distress syndrome, respiratory failure, and death. Reports on a dysregulated immune system in the severe cases call for a better characterization and understanding of the changes in the immune system. METHODS In order to dissect COVID-19-driven immune host responses, we performed RNA-seq of whole blood cell transcriptomes and granulocyte preparations from mild and severe COVID-19 patients and analyzed the data using a combination of conventional and data-driven co-expression analysis. Additionally, publicly available data was used to show the distinction from COVID-19 to other diseases. Reverse drug target prediction was used to identify known or novel drug candidates based on finding from data-driven findings. RESULTS Here, we profiled whole blood transcriptomes of 39 COVID-19 patients and 10 control donors enabling a data-driven stratification based on molecular phenotype. Neutrophil activation-associated signatures were prominently enriched in severe patient groups, which was corroborated in whole blood transcriptomes from an independent second cohort of 30 as well as in granulocyte samples from a third cohort of 16 COVID-19 patients (44 samples). Comparison of COVID-19 blood transcriptomes with those of a collection of over 3100 samples derived from 12 different viral infections, inflammatory diseases, and independent control samples revealed highly specific transcriptome signatures for COVID-19. Further, stratified transcriptomes predicted patient subgroup-specific drug candidates targeting the dysregulated systemic immune response of the host. CONCLUSIONS Our study provides novel insights in the distinct molecular subgroups or phenotypes that are not simply explained by clinical parameters. We show that whole blood transcriptomes are extremely informative for COVID-19 since they capture granulocytes which are major drivers of disease severity.
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Affiliation(s)
- Anna C Aschenbrenner
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maria Mouktaroudi
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Benjamin Krämer
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | - Marie Oestreich
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nikolaos Antonakos
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Melanie Nuesch-Germano
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Konstantina Gkizeli
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Lorenzo Bonaguro
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nico Reusch
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Kevin Baßler
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Maria Saridaki
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Rainer Knoll
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Tal Pecht
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Theodore S Kapellos
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Sarandia Doulou
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Charlotte Kröger
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Miriam Herbert
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Lisa Holsten
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Arik Horne
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Ioanna D Gemünd
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Nikoletta Rovina
- 1st Department of Pulmonary Medicine and Intensive Care Unit, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Shobhit Agrawal
- West German Genome Center (WGGC), University of Bonn, Bonn, Germany
| | - Kilian Dahm
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Martina van Uelft
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Anna Drews
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Lena Lenkeit
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Niklas Bruse
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jelle Gerretsen
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jannik Gierlich
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Matthias Becker
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Kristian Händler
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Michael Kraut
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Heidi Theis
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Simachew Mengiste
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Elena De Domenico
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Jonas Schulte-Schrepping
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Lea Seep
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jan Raabe
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | | | - Michael ToVinh
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | - Verena Keitel
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Gereon Rieke
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany
| | - Valentina Talevi
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Dirk Skowasch
- Department of Internal Medicine II, Section of Pneumology, University Hospital of Bonn (UKB), Bonn, Germany
| | - N Ahmad Aziz
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Neurology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Peter Pickkers
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frank L van de Veerdonk
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands.,Immunology & Metabolism, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Matthijs Kox
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Monique M B Breteler
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Jacob Nattermann
- Department I of Internal Medicine, University Hospital of Bonn (UKB), Bonn, Germany.,German Center for Infection Research (DZIF), Bonn, Germany
| | - Antonia Koutsoukou
- 1st Department of Pulmonary Medicine and Intensive Care Unit, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | | | - Thomas Ulas
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany. .,PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany.
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24
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Enderes J, Mallesh S, Schneider R, Hupa KJ, Lysson M, Schneiker B, Händler K, Schlotmann B, Günther P, Schultze JL, Kalff JC, Wehner S. A Population of Radio-Resistant Macrophages in the Deep Myenteric Plexus Contributes to Postoperative Ileus Via Toll-Like Receptor 3 Signaling. Front Immunol 2021; 11:581111. [PMID: 33519804 PMCID: PMC7838642 DOI: 10.3389/fimmu.2020.581111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
Postoperative ileus (POI) is triggered by an innate immune response in the muscularis externa (ME) and is accompanied by bacterial translocation. Bacteria can trigger an innate immune response via toll-like receptor (TLR) activation, but the latter's contribution to POI has been disproved for several TLRs, including TLR2 and TLR4. Herein we investigated the role of double-stranded RNA detection via TLR3 and TIR-domain-containing adapter-inducing interferon-β (TRIF) signaling pathway in POI. POI was induced by small bowel intestinal manipulation in wt, TRIF-/-, TLR3-/-, type I interferon receptor-/- and interferon-β reporter mice, all on C57BL/6 background, and POI severity was quantified by gene expression analysis, gastrointestinal transit and leukocyte extravasation into the ME. TRIF/TLR3 deficiency reduced postoperative ME inflammation and prevented POI. With bone marrow transplantation, RNA-sequencing, flow cytometry and immunohistochemistry we revealed a distinct TLR3-expressing radio-resistant MHCIIhiCX3CR1- IBA-1+ resident macrophage population within the deep myenteric plexus. TLR3 deficiency in these cells, but not in MHCIIhiCX3CR1+ macrophages, reduced cytokine expression in POI. While this might not be an exclusive macrophage-privileged pathway, the TLR3/TRIF axis contributes to proinflammatory cytokine production in MHCIIhiCX3CR1- IBA-1+ macrophages during POI. Deficiency in TLR3/TRIF protects mice from POI. These data suggest that TLR3 antagonism may prevent POI in humans.
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Affiliation(s)
- Jana Enderes
- Department of Surgery, Division of Immune Pathophysiology, University Hospital Bonn, Bonn, Germany
| | - Shilpashree Mallesh
- Department of Surgery, Division of Immune Pathophysiology, University Hospital Bonn, Bonn, Germany
| | - Reiner Schneider
- Department of Surgery, Division of Immune Pathophysiology, University Hospital Bonn, Bonn, Germany
| | - Kristof J Hupa
- Department of Surgery, Division of Immune Pathophysiology, University Hospital Bonn, Bonn, Germany
| | - Mariola Lysson
- Department of Surgery, Division of Immune Pathophysiology, University Hospital Bonn, Bonn, Germany
| | - Bianca Schneiker
- Department of Surgery, Division of Immune Pathophysiology, University Hospital Bonn, Bonn, Germany
| | - Kristian Händler
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany
| | - Balthasar Schlotmann
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Patrick Günther
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Jörg C Kalff
- Department of Surgery, Division of Immune Pathophysiology, University Hospital Bonn, Bonn, Germany
| | - Sven Wehner
- Department of Surgery, Division of Immune Pathophysiology, University Hospital Bonn, Bonn, Germany
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25
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Gerber JP, Russ J, Chandrasekar V, Offermann N, Lee HM, Spear S, Guzzi N, Maida S, Pattabiraman S, Zhang R, Kayvanjoo AH, Datta P, Kasturiarachchi J, Sposito T, Izotova N, Händler K, Adams PD, Marafioti T, Enver T, Wenzel J, Beyer M, Mass E, Bellodi C, Schultze JL, Capasso M, Nimmo R, Salomoni P. Aberrant chromatin landscape following loss of the H3.3 chaperone Daxx in haematopoietic precursors leads to Pu.1-mediated neutrophilia and inflammation. Nat Cell Biol 2021; 23:1224-1239. [PMID: 34876685 PMCID: PMC8683376 DOI: 10.1038/s41556-021-00774-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/14/2021] [Indexed: 12/25/2022]
Abstract
Defective silencing of retrotransposable elements has been linked to inflammageing, cancer and autoimmune diseases. However, the underlying mechanisms are only partially understood. Here we implicate the histone H3.3 chaperone Daxx, a retrotransposable element repressor inactivated in myeloid leukaemia and other neoplasms, in protection from inflammatory disease. Loss of Daxx alters the chromatin landscape, H3.3 distribution and histone marks of haematopoietic progenitors, leading to engagement of a Pu.1-dependent transcriptional programme for myelopoiesis at the expense of B-cell differentiation. This causes neutrophilia and inflammation, predisposing mice to develop an autoinflammatory skin disease. While these molecular and phenotypic perturbations are in part reverted in animals lacking both Pu.1 and Daxx, haematopoietic progenitors in these mice show unique chromatin and transcriptome alterations, suggesting an interaction between these two pathways. Overall, our findings implicate retrotransposable element silencing in haematopoiesis and suggest a cross-talk between the H3.3 loading machinery and the pioneer transcription factor Pu.1.
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Affiliation(s)
- Julia P. Gerber
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany ,grid.83440.3b0000000121901201Department of Cancer Biology, UCL Cancer Institute, London, UK
| | - Jenny Russ
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Vijay Chandrasekar
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Nina Offermann
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Hang-Mao Lee
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Sarah Spear
- grid.4868.20000 0001 2171 1133Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Nicola Guzzi
- grid.4514.40000 0001 0930 2361Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Simona Maida
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Ruoyu Zhang
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Amir H. Kayvanjoo
- grid.10388.320000 0001 2240 3300Life and Medical Sciences (LIMES) Institute, Developmental Biology of the Immune System, University of Bonn, Bonn, Germany
| | - Preeta Datta
- grid.83440.3b0000000121901201Department of Cancer Biology, UCL Cancer Institute, London, UK
| | - Jagath Kasturiarachchi
- grid.83440.3b0000000121901201Department of Cancer Biology, UCL Cancer Institute, London, UK
| | - Teresa Sposito
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Natalia Izotova
- grid.83440.3b0000000121901201Department of Cancer Biology, UCL Cancer Institute, London, UK
| | - Kristian Händler
- grid.10388.320000 0001 2240 3300Platform for Single Cell Genomics and Epigenomics (PRECISE) at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Peter D. Adams
- grid.479509.60000 0001 0163 8573Sanford Burnham Prebys Medical Discovery Institute, La Jolla, USA
| | - Teresa Marafioti
- grid.83440.3b0000000121901201Department of Cancer Biology, UCL Cancer Institute, London, UK ,grid.83440.3b0000000121901201Department of Pathology, University College London, London, UK
| | - Tariq Enver
- grid.83440.3b0000000121901201Department of Cancer Biology, UCL Cancer Institute, London, UK
| | - Jörg Wenzel
- Department of Dermatology and Allergy, University Medical Center, Bonn, Germany
| | - Marc Beyer
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany ,grid.10388.320000 0001 2240 3300Platform for Single Cell Genomics and Epigenomics (PRECISE) at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Elvira Mass
- grid.10388.320000 0001 2240 3300Life and Medical Sciences (LIMES) Institute, Developmental Biology of the Immune System, University of Bonn, Bonn, Germany
| | - Cristian Bellodi
- grid.4514.40000 0001 0930 2361Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Joachim L. Schultze
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany ,grid.10388.320000 0001 2240 3300Platform for Single Cell Genomics and Epigenomics (PRECISE) at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany ,grid.10388.320000 0001 2240 3300Genomics and Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany
| | - Melania Capasso
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany ,grid.4868.20000 0001 2171 1133Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Rachael Nimmo
- grid.83440.3b0000000121901201Department of Cancer Biology, UCL Cancer Institute, London, UK
| | - Paolo Salomoni
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany. .,Department of Cancer Biology, UCL Cancer Institute, London, UK.
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26
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De Domenico E, Bonaguro L, Schulte-Schrepping J, Becker M, Händler K, Schultze JL. Optimized workflow for single-cell transcriptomics on infectious diseases including COVID-19. STAR Protoc 2020; 1:100233. [PMID: 33377120 PMCID: PMC7757730 DOI: 10.1016/j.xpro.2020.100233] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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).
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Affiliation(s)
- Elena De Domenico
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Lorenzo Bonaguro
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jonas Schulte-Schrepping
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Matthias Becker
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Kristian Händler
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Joachim L. Schultze
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Corresponding author
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27
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Schulte-Schrepping J, Reusch N, Paclik D, Baßler K, Schlickeiser S, Zhang B, Krämer B, Krammer T, Brumhard S, Bonaguro L, De Domenico E, Wendisch D, Grasshoff M, Kapellos TS, Beckstette M, Pecht T, Saglam A, Dietrich O, Mei HE, Schulz AR, Conrad C, Kunkel D, Vafadarnejad E, Xu CJ, Horne A, Herbert M, Drews A, Thibeault C, Pfeiffer M, Hippenstiel S, Hocke A, Müller-Redetzky H, Heim KM, Machleidt F, Uhrig A, Bosquillon de Jarcy L, Jürgens L, Stegemann M, Glösenkamp CR, Volk HD, Goffinet C, Landthaler M, Wyler E, Georg P, Schneider M, Dang-Heine C, Neuwinger N, Kappert K, Tauber R, Corman V, Raabe J, Kaiser KM, Vinh MT, Rieke G, Meisel C, Ulas T, Becker M, Geffers R, Witzenrath M, Drosten C, Suttorp N, von Kalle C, Kurth F, Händler K, Schultze JL, Aschenbrenner AC, Li Y, Nattermann J, Sawitzki B, Saliba AE, Sander LE. Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment. Cell 2020; 182:1419-1440.e23. [PMID: 32810438 PMCID: PMC7405822 DOI: 10.1016/j.cell.2020.08.001] [Citation(s) in RCA: 908] [Impact Index Per Article: 227.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/13/2020] [Accepted: 07/31/2020] [Indexed: 02/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a mild to moderate respiratory tract infection, however, a subset of patients progress 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 remain 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 versus severe COVID-19 (242 samples from 109 individuals) over time. HLA-DRhiCD11chi 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-DRlo monocytes. Our study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and reveals profound alterations in the myeloid cell compartment associated with severe COVID-19.
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Affiliation(s)
| | - Nico Reusch
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Germany
| | - Daniela Paclik
- Institute of Medical Immunology, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Kevin Baßler
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Germany
| | - Stephan Schlickeiser
- Institute of Medical Immunology, Charité, Universitätsmedizin Berlin, Berlin, Germany; BIH Center for Regenerative Therapies, Charité, Universitätsmedizin Berlin, and Berlin Institute of Health (BIH) Berlin, Germany
| | - Bowen Zhang
- Centre for Individualised Infection Medicine (CiiM) and TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Benjamin Krämer
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Tobias Krammer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Sophia Brumhard
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Lorenzo Bonaguro
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Germany
| | - Elena De Domenico
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany
| | - Daniel Wendisch
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Grasshoff
- Centre for Individualised Infection Medicine (CiiM) and TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | | | - Michael Beckstette
- Centre for Individualised Infection Medicine (CiiM) and TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Tal Pecht
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Germany
| | - Adem Saglam
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany
| | - Oliver Dietrich
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Henrik E Mei
- Mass Cytometry Lab, DRFZ Berlin, a Leibniz Institute, Berlin, Germany
| | - Axel R Schulz
- Mass Cytometry Lab, DRFZ Berlin, a Leibniz Institute, Berlin, Germany
| | - Claudia Conrad
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Désirée Kunkel
- Flow and Mass Cytometry Core Facility, Charité, Universitätsmedizin Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Ehsan Vafadarnejad
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine (CiiM) and TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Arik Horne
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Germany
| | - Miriam Herbert
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Germany
| | - Anna Drews
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany
| | - Charlotte Thibeault
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Moritz Pfeiffer
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Hippenstiel
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL)
| | - Andreas Hocke
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL)
| | - Holger Müller-Redetzky
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Katrin-Moira Heim
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Felix Machleidt
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Alexander Uhrig
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Laure Bosquillon de Jarcy
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Linda Jürgens
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Miriam Stegemann
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph R Glösenkamp
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Hans-Dieter Volk
- Institute of Medical Immunology, Charité, Universitätsmedizin Berlin, Berlin, Germany; BIH Center for Regenerative Therapies, Charité, Universitätsmedizin Berlin, and Berlin Institute of Health (BIH) Berlin, Germany; Department of Immunology, Labor Berlin-Charité Vivantes, Berlin, Germany
| | - Christine Goffinet
- Institute of Virology, Charité Universitätsmedizin Berlin, Berlin, Germany; Berlin Institute of Health (BIH), Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Philipp Georg
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Maria Schneider
- Institute of Medical Immunology, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Chantip Dang-Heine
- Clinical Study Center (CSC), Charité, Universitätsmedizin Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Nick Neuwinger
- Department of Immunology, Labor Berlin-Charité Vivantes, Berlin, Germany; Institute of Laboratory Medicine, Clinical Chemistry, and Pathobiochemistry, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Kai Kappert
- Department of Immunology, Labor Berlin-Charité Vivantes, Berlin, Germany; Institute of Laboratory Medicine, Clinical Chemistry, and Pathobiochemistry, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Rudolf Tauber
- Department of Immunology, Labor Berlin-Charité Vivantes, Berlin, Germany; Institute of Laboratory Medicine, Clinical Chemistry, and Pathobiochemistry, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Victor Corman
- Institute of Virology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Jan Raabe
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Kim Melanie Kaiser
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Michael To Vinh
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Gereon Rieke
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Christian Meisel
- Institute of Medical Immunology, Charité, Universitätsmedizin Berlin, Berlin, Germany; Department of Immunology, Labor Berlin-Charité Vivantes, Berlin, Germany
| | - Thomas Ulas
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany
| | - Matthias Becker
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany
| | - Robert Geffers
- Genome Analytics, Helmholtz-Center for Infection Research (HZI), Braunschweig, Germany
| | - Martin Witzenrath
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL)
| | - Christian Drosten
- Institute of Virology, Charité Universitätsmedizin Berlin, Berlin, Germany; German Center for Infection Research (DZIF)
| | - Norbert Suttorp
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL)
| | - Christof von Kalle
- Clinical Study Center (CSC), Charité, Universitätsmedizin Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; I. Department of Medicine, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Kristian Händler
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany.
| | - Anna C Aschenbrenner
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Yang Li
- Centre for Individualised Infection Medicine (CiiM) and TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jacob Nattermann
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany; German Center for Infection Research (DZIF)
| | - Birgit Sawitzki
- Institute of Medical Immunology, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Leif Erik Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL)
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28
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Cirovic B, de Bree LCJ, Groh L, Blok BA, Chan J, van der Velden WJFM, Bremmers MEJ, van Crevel R, Händler K, Picelli S, Schulte-Schrepping J, Klee K, Oosting M, Koeken VACM, van Ingen J, Li Y, Benn CS, Schultze JL, Joosten LAB, Curtis N, Netea MG, Schlitzer A. BCG Vaccination in Humans Elicits Trained Immunity via the Hematopoietic Progenitor Compartment. Cell Host Microbe 2020; 28:322-334.e5. [PMID: 32544459 PMCID: PMC7295478 DOI: 10.1016/j.chom.2020.05.014] [Citation(s) in RCA: 215] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/16/2020] [Accepted: 05/12/2020] [Indexed: 01/13/2023]
Abstract
Induction of trained immunity by Bacille-Calmette-Guérin (BCG) vaccination mediates beneficial heterologous effects, but the mechanisms underlying its persistence and magnitude remain elusive. In this study, we show that BCG vaccination in healthy human volunteers induces a persistent transcriptional program connected to myeloid cell development and function within the hematopoietic stem and progenitor cell (HSPC) compartment in the bone marrow. We identify hepatic nuclear factor (HNF) family members 1a and b as crucial regulators of this transcriptional shift. These findings are corroborated by higher granulocyte numbers in BCG-vaccinated infants, HNF1 SNP variants that correlate with trained immunity, and elevated serum concentrations of the HNF1 target alpha-1 antitrypsin. Additionally, transcriptomic HSPC remodeling was epigenetically conveyed to peripheral CD14+ monocytes, displaying an activated transcriptional signature three months after BCG vaccination. Taken together, transcriptomic, epigenomic, and functional reprogramming of HSPCs and peripheral monocytes is a hallmark of BCG-induced trained immunity in humans.
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Affiliation(s)
- Branko Cirovic
- Quantitative Systems Biology, Life & Medical Sciences Institute, University of Bonn, 53115 Bonn, Germany
| | - L Charlotte J de Bree
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, 6526 GA Nijmegen, the Netherlands; Research Center for Vitamins and Vaccines, Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark; Odense Patient Data Explorative Network, University of Southern Denmark/Odense University Hospital, Odense, Denmark
| | - Laszlo Groh
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, 6526 GA Nijmegen, the Netherlands
| | - Bas A Blok
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, 6526 GA Nijmegen, the Netherlands; Research Center for Vitamins and Vaccines, Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark; Odense Patient Data Explorative Network, University of Southern Denmark/Odense University Hospital, Odense, Denmark
| | - Joyce Chan
- Department of Paediatrics, The University of Melbourne & Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Parkville, Australia
| | | | - M E J Bremmers
- Department of Haematology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Reinout van Crevel
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, 6526 GA Nijmegen, the Netherlands
| | - Kristian Händler
- Single Cell Genomics and Epigenomics Unit at the German Center for Neurodegenerative Diseases and the University of Bonn, 53175 Bonn, Germany
| | - Simone Picelli
- Single Cell Genomics and Epigenomics Unit at the German Center for Neurodegenerative Diseases and the University of Bonn, 53175 Bonn, Germany
| | - Jonas Schulte-Schrepping
- Genomics and Immunoregulation, Life & Medical Sciences Institute, University of Bonn, 53115 Bonn, Germany
| | - Kathrin Klee
- Genomics and Immunoregulation, Life & Medical Sciences Institute, University of Bonn, 53115 Bonn, Germany
| | - Marije Oosting
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, 6526 GA Nijmegen, the Netherlands
| | - Valerie A C M Koeken
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, 6526 GA Nijmegen, the Netherlands
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Yang Li
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, 6526 GA Nijmegen, the Netherlands; Centre for Individualised Infection Medicine (CiiM) & TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Christine S Benn
- Research Center for Vitamins and Vaccines, Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark; Odense Patient Data Explorative Network, University of Southern Denmark/Odense University Hospital, Odense, Denmark
| | - Joachim L Schultze
- Single Cell Genomics and Epigenomics Unit at the German Center for Neurodegenerative Diseases and the University of Bonn, 53175 Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences Institute, University of Bonn, 53115 Bonn, Germany
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, 6526 GA Nijmegen, the Netherlands
| | - Nigel Curtis
- Department of Paediatrics, The University of Melbourne & Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Parkville, Australia
| | - Mihai G Netea
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, 6526 GA Nijmegen, the Netherlands; Immunology and Metabolism, Life & Medical Sciences Institute, University of Bonn, 53115 Bonn, Germany.
| | - Andreas Schlitzer
- Quantitative Systems Biology, Life & Medical Sciences Institute, University of Bonn, 53115 Bonn, Germany; Single Cell Genomics and Epigenomics Unit at the German Center for Neurodegenerative Diseases and the University of Bonn, 53175 Bonn, Germany.
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29
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Werner Y, Mass E, Ashok Kumar P, Ulas T, Händler K, Horne A, Klee K, Lupp A, Schütz D, Saaber F, Redecker C, Schultze JL, Geissmann F, Stumm R. Cxcr4 distinguishes HSC-derived monocytes from microglia and reveals monocyte immune responses to experimental stroke. Nat Neurosci 2020; 23:351-362. [PMID: 32042176 PMCID: PMC7523735 DOI: 10.1038/s41593-020-0585-y] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 01/02/2020] [Indexed: 12/26/2022]
Abstract
Monocyte-derived and tissue-resident macrophages are ontogenetically distinct components of the innate immune system. Assessment of their respective functions in pathology is complicated by changes to the macrophage phenotype during inflammation. Here we find that Cxcr4-CreER enables permanent genetic labeling of hematopoietic stem cells (HSCs) and distinguishes HSC-derived monocytes from microglia and other tissue-resident macrophages. By combining Cxcr4-CreER-mediated lineage tracing with Cxcr4 inhibition or conditional Cxcr4 ablation in photothrombotic stroke, we find that Cxcr4 promotes initial monocyte infiltration and subsequent territorial restriction of monocyte-derived macrophages to infarct tissue. After transient focal ischemia, Cxcr4 deficiency reduces monocyte infiltration and blunts the expression of pattern recognition and defense response genes in monocyte-derived macrophages. This is associated with an altered microglial response and deteriorated outcomes. Thus, Cxcr4 is essential for an innate-immune-system-mediated defense response after cerebral ischemia. We further propose Cxcr4-CreER as a universal tool to study functions of HSC-derived cells.
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Affiliation(s)
- Yves Werner
- Institute of Pharmacology and Toxicology, Jena University Hospital, Jena, Germany
| | - Elvira Mass
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Developmental Biology of the Immune System, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany.
| | - Praveen Ashok Kumar
- Institute of Pharmacology and Toxicology, Jena University Hospital, Jena, Germany
| | - Thomas Ulas
- Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases and University of Bonn, Bonn, Germany
| | - Kristian Händler
- Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases and University of Bonn, Bonn, Germany
| | - Arik Horne
- Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Kathrin Klee
- Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Amelie Lupp
- Institute of Pharmacology and Toxicology, Jena University Hospital, Jena, Germany
| | - Dagmar Schütz
- Institute of Pharmacology and Toxicology, Jena University Hospital, Jena, Germany
| | - Friederike Saaber
- Institute of Pharmacology and Toxicology, Jena University Hospital, Jena, Germany
| | | | - Joachim L Schultze
- Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases and University of Bonn, Bonn, Germany
| | - Frederic Geissmann
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Ralf Stumm
- Institute of Pharmacology and Toxicology, Jena University Hospital, Jena, Germany.
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30
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Hatzioannou A, Banos A, Sakelaropoulos T, Fedonidis C, Vidali MS, Köhne M, Händler K, Boon L, Henriques A, Koliaraki V, Georgiadis P, Zoidakis J, Termentzi A, Beyer M, Chavakis T, Boumpas D, Tsirigos A, Verginis P. An intrinsic role of IL-33 in T reg cell-mediated tumor immunoevasion. Nat Immunol 2019; 21:75-85. [PMID: 31844326 PMCID: PMC7030950 DOI: 10.1038/s41590-019-0555-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 10/31/2019] [Indexed: 02/08/2023]
Abstract
Regulatory T (Treg) cells accumulate into tumors hindering the success of cancer immunotherapy. Yet, therapeutic targeting of Treg cells shows limited efficacy or leads to autoimmunity. The molecular mechanisms that guide Treg cell stability in tumors, remain elusive. Herein, we identify a cell-intrinsic role of the alarmin IL-33 in the functional stability of Treg cells. Specifically, IL-33-deficient Treg cells demonstrated attenuated suppressive properties in vivo and facilitated tumor regression in an ST2 (IL-33 receptor)-independent fashion. Upon activation, Il33–/– Treg cells exhibited epigenetic reprogramming with increased chromatin accessibility of the Ifng locus leading to elevated interferon-γ (IFN-γ) production in an NF-κB–T-bet-dependent manner. IFN-γ was essential for Treg cell defective function since its ablation restored Il33–/– Treg cell suppressive properties. Importantly, genetic ablation of Il33 potentiated the therapeutic effect of immunotherapy. Our findings reveal a novel and therapeutically important intrinsic role of IL-33 in Treg cell stability in cancer.
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Affiliation(s)
- Aikaterini Hatzioannou
- Center of Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Aggelos Banos
- Center of Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Theodore Sakelaropoulos
- Applied Bioinformatics Laboratories and Department of Pathology, New York University School of Medicine, New York, NY, USA.,Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Constantinos Fedonidis
- Center of Basic Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Maria-Sophia Vidali
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Maren Köhne
- Molecular Immunology in Neurodegeneration, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Kristian Händler
- PRECISE, Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | | | - Ana Henriques
- Department of Immunology, Biomedical Sciences Research Centre 'Alexander Fleming', Vari, Greece
| | - Vasiliki Koliaraki
- Department of Immunology, Biomedical Sciences Research Centre 'Alexander Fleming', Vari, Greece
| | - Panagiotis Georgiadis
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Jerome Zoidakis
- Biotechnology Division, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Aikaterini Termentzi
- Department of Pesticides Control and Phytopharmacy, Benaki Phytopathological Institute, Athens, Greece
| | - Marc Beyer
- Molecular Immunology in Neurodegeneration, German Center for Neurodegenerative Diseases, Bonn, Germany.,PRECISE, Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Triantafyllos Chavakis
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany.,National Center for Tumor Diseases, Partner Site Dresden and German Cancer Research Center, Heidelberg, Germany
| | - Dimitrios Boumpas
- Center of Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece.,Joint Rheumatology Program, 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Aristotelis Tsirigos
- Applied Bioinformatics Laboratories and Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Panayotis Verginis
- Center of Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece. .,Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany.
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31
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Rakers C, Schleif M, Blank N, Matušková H, Ulas T, Händler K, Torres SV, Schumacher T, Tai K, Schultze JL, Jackson WS, Petzold GC. Stroke target identification guided by astrocyte transcriptome analysis. Glia 2018; 67:619-633. [DOI: 10.1002/glia.23544] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Cordula Rakers
- German Center for Neurodegenerative Diseases (DZNE); Bonn Germany
| | - Melvin Schleif
- German Center for Neurodegenerative Diseases (DZNE); Bonn Germany
| | - Nelli Blank
- German Center for Neurodegenerative Diseases (DZNE); Bonn Germany
| | - Hana Matušková
- German Center for Neurodegenerative Diseases (DZNE); Bonn Germany
- Department of Neurology; University Hospital Bonn; Bonn Germany
| | - Thomas Ulas
- Genomics and Immunoregulation; LIMES-Institute, University of Bonn; Germany
| | - Kristian Händler
- Genomics and Immunoregulation; LIMES-Institute, University of Bonn; Germany
| | | | - Toni Schumacher
- German Center for Neurodegenerative Diseases (DZNE); Bonn Germany
| | - Khalid Tai
- German Center for Neurodegenerative Diseases (DZNE); Bonn Germany
| | - Joachim L. Schultze
- German Center for Neurodegenerative Diseases (DZNE); Bonn Germany
- Genomics and Immunoregulation; LIMES-Institute, University of Bonn; Germany
| | | | - Gabor C. Petzold
- German Center for Neurodegenerative Diseases (DZNE); Bonn Germany
- Department of Neurology; University Hospital Bonn; Bonn Germany
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32
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Pfeiffer F, Gröber C, Blank M, Händler K, Beyer M, Schultze JL, Mayer G. Systematic evaluation of error rates and causes in short samples in next-generation sequencing. Sci Rep 2018; 8:10950. [PMID: 30026539 PMCID: PMC6053417 DOI: 10.1038/s41598-018-29325-6] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/09/2018] [Indexed: 01/08/2023] Open
Abstract
Next-generation sequencing (NGS) is the method of choice when large numbers of sequences have to be obtained. While the technique is widely applied, varying error rates have been observed. We analysed millions of reads obtained after sequencing of one single sequence on an Illumina sequencer. According to our analysis, the index-PCR for sample preparation has no effect on the observed error rate, even though PCR is traditionally seen as one of the major contributors to enhanced error rates in NGS. In addition, we observed very persistent pre-phasing effects although the base calling software corrects for these. Removal of shortened sequences abolished these effects and allowed analysis of the actual mutations. The average error rate determined was 0.24 ± 0.06% per base and the percentage of mutated sequences was found to be 6.4 ± 1.24%. Constant regions at the 5'- and 3'-end, e.g., primer binding sites used in in vitro selection procedures seem to have no effect on mutation rates and re-sequencing of samples obtains very reproducible results. As phasing effects and other sequencing problems vary between equipment and individual setups, we recommend evaluation of error rates and types to all NGS-users to improve the quality and analysis of NGS data.
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Affiliation(s)
- Franziska Pfeiffer
- University of Bonn, LIMES Institute, Chemical Biology, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Carsten Gröber
- AptaIT GmbH, Am Klopferspitz 19A, 82152, Planegg, Germany
| | - Michael Blank
- AptaIT GmbH, Am Klopferspitz 19A, 82152, Planegg, Germany
| | - Kristian Händler
- University of Bonn, LIMES Institute, Genomics and Immunoregulation, Carl-Troll-Str. 31, 53115, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE) and University of Bonn, Platform for Single Cell Genomics and Epigenomics, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Marc Beyer
- University of Bonn, LIMES Institute, Genomics and Immunoregulation, Carl-Troll-Str. 31, 53115, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE) and University of Bonn, Platform for Single Cell Genomics and Epigenomics, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
- DZNE, Molecular Immunology in Neurodegeneration, Sigmund-Freud-Str. 27, 53127, Bonn, Germany
| | - Joachim L Schultze
- University of Bonn, LIMES Institute, Genomics and Immunoregulation, Carl-Troll-Str. 31, 53115, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE) and University of Bonn, Platform for Single Cell Genomics and Epigenomics, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Günter Mayer
- University of Bonn, LIMES Institute, Chemical Biology, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany.
- Center of Aptamer Research and Development, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany.
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33
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Sander J, Schmidt SV, Cirovic B, McGovern N, Papantonopoulou O, Hardt AL, Aschenbrenner AC, Kreer C, Quast T, Xu AM, Schmidleithner LM, Theis H, Thi Huong LD, Sumatoh HRB, Lauterbach MAR, Schulte-Schrepping J, Günther P, Xue J, Baßler K, Ulas T, Klee K, Katzmarski N, Herresthal S, Krebs W, Martin B, Latz E, Händler K, Kraut M, Kolanus W, Beyer M, Falk CS, Wiegmann B, Burgdorf S, Melosh NA, Newell EW, Ginhoux F, Schlitzer A, Schultze JL. Cellular Differentiation of Human Monocytes Is Regulated by Time-Dependent Interleukin-4 Signaling and the Transcriptional Regulator NCOR2. Immunity 2017; 47:1051-1066.e12. [PMID: 29262348 PMCID: PMC5772172 DOI: 10.1016/j.immuni.2017.11.024] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 09/15/2017] [Accepted: 11/28/2017] [Indexed: 12/24/2022]
Abstract
Human in vitro generated monocyte-derived dendritic cells (moDCs) and macrophages are used clinically, e.g., to induce immunity against cancer. However, their physiological counterparts, ontogeny, transcriptional regulation, and heterogeneity remains largely unknown, hampering their clinical use. High-dimensional techniques were used to elucidate transcriptional, phenotypic, and functional differences between human in vivo and in vitro generated mononuclear phagocytes to facilitate their full potential in the clinic. We demonstrate that monocytes differentiated by macrophage colony-stimulating factor (M-CSF) or granulocyte macrophage colony-stimulating factor (GM-CSF) resembled in vivo inflammatory macrophages, while moDCs resembled in vivo inflammatory DCs. Moreover, differentiated monocytes presented with profound transcriptomic, phenotypic, and functional differences. Monocytes integrated GM-CSF and IL-4 stimulation combinatorically and temporally, resulting in a mode- and time-dependent differentiation relying on NCOR2. Finally, moDCs are phenotypically heterogeneous and therefore necessitate the use of high-dimensional phenotyping to open new possibilities for better clinical tailoring of these cellular therapies. In vitro monocyte cultures model in vivo inflammatory dendritic cells and macrophages Monocyte-derived dendritic cells integrate interleukin-4 signaling time dependently NCOR2 controls differentiation of in vitro generated monocyte-derived dendritic cells In vitro generated monocyte-derived cells are phenotypically heterogeneous
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Affiliation(s)
- Jil Sander
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Susanne V Schmidt
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Branko Cirovic
- Myeloid Cell Biology, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Naomi McGovern
- Agency for Science, Technology and Research (A(∗)STAR), Singapore Immunology Network (SIgN), 138648 Singapore, Singapore; Department of Pathology and Center for Trophoblast Research, University of Cambridge, CB2 1QP Cambridge, UK
| | | | - Anna-Lena Hardt
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Anna C Aschenbrenner
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Christoph Kreer
- Cellular Immunology, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Thomas Quast
- Molecular Immunology & Cell Biology, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Alexander M Xu
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | - Lisa M Schmidleithner
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Heidi Theis
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Lan Do Thi Huong
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Hermi Rizal Bin Sumatoh
- Agency for Science, Technology and Research (A(∗)STAR), Singapore Immunology Network (SIgN), 138648 Singapore, Singapore
| | - Mario A R Lauterbach
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | | | - Patrick Günther
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Jia Xue
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Kevin Baßler
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Thomas Ulas
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Kathrin Klee
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Natalie Katzmarski
- Myeloid Cell Biology, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Stefanie Herresthal
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Wolfgang Krebs
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Bianca Martin
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Eicke Latz
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany; Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; German Center for Neurodegenerative Diseases, 53127 Bonn, Germany
| | - Kristian Händler
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Michael Kraut
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Waldemar Kolanus
- Molecular Immunology & Cell Biology, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Marc Beyer
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany; Molecular Immunology, German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Str. 27, 53127 Bonn, Germany
| | - Christine S Falk
- Institute of Transplant Immunology, Integrated Research and Treatment Center Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Bettina Wiegmann
- Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover Medical School, 30625 Hannover, Germany
| | - Sven Burgdorf
- Cellular Immunology, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Nicholas A Melosh
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | - Evan W Newell
- Agency for Science, Technology and Research (A(∗)STAR), Singapore Immunology Network (SIgN), 138648 Singapore, Singapore
| | - Florent Ginhoux
- Agency for Science, Technology and Research (A(∗)STAR), Singapore Immunology Network (SIgN), 138648 Singapore, Singapore
| | - Andreas Schlitzer
- Myeloid Cell Biology, LIMES-Institute, University of Bonn, 53115 Bonn, Germany; Agency for Science, Technology and Research (A(∗)STAR), Singapore Immunology Network (SIgN), 138648 Singapore, Singapore.
| | - Joachim L Schultze
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany; Platform for Single Cell Genomics and Epigenomics (PRECISE) at the German Center for Neurodegenerative Diseases and the University of Bonn, 53127 Bonn, Germany
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34
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Fülle L, Steiner N, Funke M, Gondorf F, Pfeiffer F, Siegl J, Opitz FV, Haßel SK, Erazo AB, Schanz O, Stunden HJ, Blank M, Gröber C, Händler K, Beyer M, Weighardt H, Latz E, Schultze JL, Mayer G, Förster I. RNA Aptamers Recognizing Murine CCL17 Inhibit T Cell Chemotaxis and Reduce Contact Hypersensitivity In Vivo. Mol Ther 2017; 26:95-104. [PMID: 29103909 PMCID: PMC5763148 DOI: 10.1016/j.ymthe.2017.10.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 10/04/2017] [Accepted: 10/04/2017] [Indexed: 01/21/2023] Open
Abstract
The chemokine CCL17, mainly produced by dendritic cells (DCs) in the immune system, is involved in the pathogenesis of various inflammatory diseases. As a ligand of CCR4, CCL17 induces chemotaxis and facilitates T cell-DC interactions. We report the identification of two novel RNA aptamers, which were validated in vitro and in vivo for their capability to neutralize CCL17. Both aptamers efficiently inhibited the directed migration of the CCR4+ lymphoma line BW5147.3 toward CCL17 in a dose-dependent manner. To study the effect of these aptamers in vivo, we used a murine model of contact hypersensitivity. Systemic application of the aptamers significantly prevented ear swelling and T cell infiltration into the ears of sensitized mice after challenge with the contact sensitizer. The results of this proof-of-principle study establish aptamers as potent inhibitors of CCL17-mediated chemotaxis. Potentially, CCL17-specific aptamers may be used therapeutically in humans to treat or prevent allergic and inflammatory diseases.
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Affiliation(s)
- Lorenz Fülle
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
| | - Nancy Steiner
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
| | - Markus Funke
- Chemical Biology and Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany; Centre of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Fabian Gondorf
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
| | - Franziska Pfeiffer
- Chemical Biology and Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany; Centre of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Julia Siegl
- Chemical Biology and Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany; Centre of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Friederike V Opitz
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
| | - Silvana K Haßel
- Chemical Biology and Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany; Centre of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Anna Belen Erazo
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
| | - Oliver Schanz
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
| | - H James Stunden
- Institute of Innate Immunity, University Hospital Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Michael Blank
- AptaIT, Am Klopferspitz 19a, 82152 Planegg-Martinsried, Germany
| | - Carsten Gröber
- AptaIT, Am Klopferspitz 19a, 82152 Planegg-Martinsried, Germany
| | - Kristian Händler
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany; Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Sigmund-Freud-Straße 27, 53127 Bonn, Germany
| | - Marc Beyer
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany; Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Sigmund-Freud-Straße 27, 53127 Bonn, Germany; Molecular Immunology in Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Straße 27, 53127 Bonn, Germany
| | - Heike Weighardt
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
| | - Eicke Latz
- Institute of Innate Immunity, University Hospital Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Joachim L Schultze
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany; Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Sigmund-Freud-Straße 27, 53127 Bonn, Germany
| | - Günter Mayer
- Chemical Biology and Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany; Centre of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
| | - Irmgard Förster
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany.
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35
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See P, Dutertre CA, Chen J, Günther P, McGovern N, Irac SE, Gunawan M, Beyer M, Händler K, Duan K, Sumatoh HRB, Ruffin N, Jouve M, Gea-Mallorquí E, Hennekam RCM, Lim T, Yip CC, Wen M, Malleret B, Low I, Shadan NB, Fen CFS, Tay A, Lum J, Zolezzi F, Larbi A, Poidinger M, Chan JKY, Chen Q, Rénia L, Haniffa M, Benaroch P, Schlitzer A, Schultze JL, Newell EW, Ginhoux F. Mapping the human DC lineage through the integration of high-dimensional techniques. Science 2017; 356:science.aag3009. [PMID: 28473638 DOI: 10.1126/science.aag3009] [Citation(s) in RCA: 373] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 04/25/2017] [Indexed: 12/16/2022]
Abstract
Dendritic cells (DC) are professional antigen-presenting cells that orchestrate immune responses. The human DC population comprises two main functionally specialized lineages, whose origins and differentiation pathways remain incompletely defined. Here, we combine two high-dimensional technologies-single-cell messenger RNA sequencing (scmRNAseq) and cytometry by time-of-flight (CyTOF)-to identify human blood CD123+CD33+CD45RA+ DC precursors (pre-DC). Pre-DC share surface markers with plasmacytoid DC (pDC) but have distinct functional properties that were previously attributed to pDC. Tracing the differentiation of DC from the bone marrow to the peripheral blood revealed that the pre-DC compartment contains distinct lineage-committed subpopulations, including one early uncommitted CD123high pre-DC subset and two CD45RA+CD123low lineage-committed subsets exhibiting functional differences. The discovery of multiple committed pre-DC populations opens promising new avenues for the therapeutic exploitation of DC subset-specific targeting.
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Affiliation(s)
- Peter See
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Charles-Antoine Dutertre
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore.,Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857 Singapore
| | - Jinmiao Chen
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Patrick Günther
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 32115 Bonn, Germany
| | - Naomi McGovern
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Sergio Erdal Irac
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857 Singapore
| | - Merry Gunawan
- Institute of Cellular Medicine, Newcastle University, Newcastle, UK
| | - Marc Beyer
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 32115 Bonn, Germany.,Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, 53175 Bonn, Germany
| | - Kristian Händler
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 32115 Bonn, Germany
| | - Kaibo Duan
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Hermi Rizal Bin Sumatoh
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Nicolas Ruffin
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, INSERM U 932, F-75005, Paris, France
| | - Mabel Jouve
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, INSERM U 932, F-75005, Paris, France
| | - Ester Gea-Mallorquí
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, INSERM U 932, F-75005, Paris, France
| | - Raoul C M Hennekam
- Department of Pediatrics, Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - Tony Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Chan Chung Yip
- Department of Health Promotion Board (HPB) and Transplant Surgery, Singapore General Hospital, Singapore
| | - Ming Wen
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857 Singapore
| | - Benoit Malleret
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ivy Low
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Nurhidaya Binte Shadan
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Charlene Foong Shu Fen
- Singapore Health Services Flow Cytometry Core Platform, 20 College Road, The Academia, Discovery Tower Level 10, Singapore 169856, Singapore
| | - Alicia Tay
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Josephine Lum
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Francesca Zolezzi
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Anis Larbi
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Michael Poidinger
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Jerry K Y Chan
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore.,Department of Reproductive Medicine, Division of Obstetrics and Gynaecology, KK Women's and Children's Hospital, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore.,Experimental Fetal Medicine Group, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Qingfeng Chen
- Humanized Mouse Unit, Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore
| | - Laurent Rénia
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle, UK
| | - Philippe Benaroch
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, INSERM U 932, F-75005, Paris, France
| | - Andreas Schlitzer
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore.,Myeloid Cell Biology, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Joachim L Schultze
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 32115 Bonn, Germany.,Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, 53175 Bonn, Germany
| | - Evan W Newell
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore.
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36
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Mass E, Ballesteros I, Farlik M, Halbritter F, Günther P, Crozet L, Jacome-Galarza CE, Händler K, Klughammer J, Kobayashi Y, Gomez-Perdiguero E, Schultze JL, Beyer M, Bock C, Geissmann F. Specification of tissue-resident macrophages during organogenesis. Science 2016; 353. [PMID: 27492475 DOI: 10.1126/science.aaf4238] [Citation(s) in RCA: 528] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 07/20/2016] [Indexed: 12/28/2022]
Abstract
Tissue-resident macrophages support embryonic development and tissue homeostasis and repair. The mechanisms that control their differentiation remain unclear. We report here that erythro-myeloid progenitors in mice generate premacrophages (pMacs) that simultaneously colonize the whole embryo from embryonic day 9.5 in a chemokine-receptor-dependent manner. The core macrophage program initiated in pMacs is rapidly diversified as expression of transcriptional regulators becomes tissue-specific in early macrophages. This process appears essential for macrophage specification and maintenance, as inactivation of Id3 impairs the development of liver macrophages and results in selective Kupffer cell deficiency in adults. We propose that macrophage differentiation is an integral part of organogenesis, as colonization of organ anlagen by pMacs is followed by their specification into tissue macrophages, hereby generating the macrophage diversity observed in postnatal tissues.
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Affiliation(s)
- Elvira Mass
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ivan Ballesteros
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Florian Halbritter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Patrick Günther
- Genomics & Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Lucile Crozet
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | | | - Kristian Händler
- Genomics & Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Johanna Klughammer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Yasuhiro Kobayashi
- Institute for Oral Science, Matsumoto Dental University, 1780 Hiro-Oka Gobara Shiojiri, Nagano, 390-0781 Japan
| | - Elisa Gomez-Perdiguero
- Centre for Molecular and Cellular Biology of Inflammation (CMCBI), King's College London, London SE1 1UL, UK
| | - Joachim L Schultze
- Genomics & Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany.,Single Cell Genomics and Epigenomics Unit at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Marc Beyer
- Genomics & Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany.,Single Cell Genomics and Epigenomics Unit at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria.,Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Frederic Geissmann
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Weill Cornell Graduate School of Medical Sciences, New York, New York, USA.,Centre for Molecular and Cellular Biology of Inflammation (CMCBI), King's College London, London SE1 1UL, UK
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37
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Shahbazi E, Moradi S, Nemati S, Satarian L, Basiri M, Gourabi H, Zare Mehrjardi N, Günther P, Lampert A, Händler K, Hatay FF, Schmidt D, Molcanyi M, Hescheler J, Schultze JL, Saric T, Baharvand H. Conversion of Human Fibroblasts to Stably Self-Renewing Neural Stem Cells with a Single Zinc-Finger Transcription Factor. Stem Cell Reports 2016; 6:539-551. [PMID: 27052315 PMCID: PMC4834053 DOI: 10.1016/j.stemcr.2016.02.013] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 02/19/2016] [Accepted: 02/22/2016] [Indexed: 01/08/2023] Open
Abstract
Direct conversion of somatic cells into neural stem cells (NSCs) by defined factors holds great promise for mechanistic studies, drug screening, and potential cell therapies for different neurodegenerative diseases. Here, we report that a single zinc-finger transcription factor, Zfp521, is sufficient for direct conversion of human fibroblasts into long-term self-renewable and multipotent NSCs. In vitro, Zfp521-induced NSCs maintained their characteristics in the absence of exogenous factor expression and exhibited morphological, molecular, developmental, and functional properties that were similar to control NSCs. In addition, the single-seeded induced NSCs were able to form NSC colonies with efficiency comparable with control NSCs and expressed NSC markers. The converted cells were capable of surviving, migrating, and attaining neural phenotypes after transplantation into neonatal mouse and adult rat brains, without forming tumors. Moreover, the Zfp521-induced NSCs predominantly expressed rostral genes. Our results suggest a facilitated approach for establishing human NSCs through Zfp521-driven conversion of fibroblasts. ZFP521 can directly convert human fetal, neonatal, and adult fibroblasts into NSCs iNSCs exhibit NSC properties, i.e., markers, long-term self-renewal, and tripotency ZFP521-iNSCs predominantly express rostral markers Single-seeded ZFP521-iNSCs are clonogenically comparable with control NSCs
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Affiliation(s)
- Ebrahim Shahbazi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran
| | - Sharif Moradi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran
| | - Shiva Nemati
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran
| | - Leila Satarian
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran
| | - Mohsen Basiri
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran
| | - Hamid Gourabi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran 1665659911, Iran
| | - Narges Zare Mehrjardi
- Center for Physiology and Pathophysiology, Institute for Neurophysiology, Medical Faculty, University of Cologne, Cologne 50931, Germany
| | - Patrick Günther
- Department for Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn 53115, Germany
| | - Angelika Lampert
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-University of Erlangen- Nürnberg, Erlangen 91054, Germany; Institute of Physiology, RWTH, Aachen University, Aachen 52074, Germany
| | - Kristian Händler
- Department for Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn 53115, Germany
| | - Firuze Fulya Hatay
- Center for Physiology and Pathophysiology, Institute for Neurophysiology, Medical Faculty, University of Cologne, Cologne 50931, Germany
| | - Diana Schmidt
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-University of Erlangen- Nürnberg, Erlangen 91054, Germany; IZKF Junior Research Group and BMBF Research Group Neuroscience, IZKF, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Marek Molcanyi
- Center for Physiology and Pathophysiology, Institute for Neurophysiology, Medical Faculty, University of Cologne, Cologne 50931, Germany
| | - Jürgen Hescheler
- Center for Physiology and Pathophysiology, Institute for Neurophysiology, Medical Faculty, University of Cologne, Cologne 50931, Germany
| | - Joachim L Schultze
- Department for Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn 53115, Germany
| | - Tomo Saric
- Center for Physiology and Pathophysiology, Institute for Neurophysiology, Medical Faculty, University of Cologne, Cologne 50931, Germany.
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran; Department of Developmental Biology, University of Science and Culture, ACECR, Tehran 1461968151, Iran.
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Finn S, Rogers L, Händler K, McClure P, Amézquita A, Hinton JCD, Fanning S. Exposure of Salmonella enterica Serovar Typhimurium to Three Humectants Used in the Food Industry Induces Different Osmoadaptation Systems. Appl Environ Microbiol 2015; 81:6800-11. [PMID: 26209672 PMCID: PMC4561688 DOI: 10.1128/aem.01379-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/15/2015] [Indexed: 11/22/2022] Open
Abstract
Common salt (NaCl) is frequently used by the food industry to add flavor and to act as a humectant in order to reduce the water content of a food product. The improved health awareness of consumers is leading to a demand for food products with reduced salt content; thus, manufacturers require alternative water activity-reducing agents which elicit the same general effects as NaCl. Two examples include KCl and glycerol. These agents lower the water activity of a food matrix and also contribute to limit the growth of the microbiota, including foodborne pathogens. Little is currently known about how foodborne pathogens respond to these water activity-lowering agents. Here we examined the response of Salmonella enterica serovar Typhimurium 4/74 to NaCl, KCl, and glycerol at three time points, using a constant water activity level, compared with the response of a control inoculum. All conditions induced the upregulation of gluconate metabolic genes after 6 h of exposure. Bacteria exposed to NaCl and KCl demonstrated the upregulation of the osmoprotective transporter mechanisms encoded by the proP, proU, and osmU (STM1491 to STM1494) genes. Glycerol exposure elicited the downregulation of these osmoadaptive mechanisms but stimulated an increase in lipopolysaccharide and membrane protein-associated genes after 1 h. The most extensive changes in gene expression occurred following exposure to KCl. Because many of these genes were of unknown function, further characterization may identify KCl-specific adaptive processes that are not stimulated by NaCl. This study shows that the response of S. Typhimurium to different humectants does not simply reflect reduced water activity and likely involves systems that are linked to specific humectants.
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Affiliation(s)
- Sarah Finn
- UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Lisa Rogers
- Conway Institute, UCD School of Biomolecular & Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Kristian Händler
- Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Peter McClure
- Unilever, Safety and Environmental Assurance Centre, Sharnbrook, Bedfordshire, United Kingdom
| | - Alejandro Amézquita
- Unilever, Safety and Environmental Assurance Centre, Sharnbrook, Bedfordshire, United Kingdom
| | - Jay C D Hinton
- Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Séamus Fanning
- UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin, Belfield, Dublin, Ireland Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland
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39
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Condell O, Power KA, Händler K, Finn S, Sheridan A, Sergeant K, Renaut J, Burgess CM, Hinton JCD, Nally JE, Fanning S. Comparative analysis of Salmonella susceptibility and tolerance to the biocide chlorhexidine identifies a complex cellular defense network. Front Microbiol 2014; 5:373. [PMID: 25136333 PMCID: PMC4117984 DOI: 10.3389/fmicb.2014.00373] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 07/03/2014] [Indexed: 12/04/2022] Open
Abstract
Chlorhexidine is one of the most widely used biocides in health and agricultural settings as well as in the modern food industry. It is a cationic biocide of the biguanide class. Details of its mechanism of action are largely unknown. The frequent use of chlorhexidine has been questioned recently, amidst concerns that an overuse of this compound may select for bacteria displaying an altered susceptibility to antimicrobials, including clinically important anti-bacterial agents. We generated a Salmonella enterica serovar Typhimurium isolate (ST24CHX) that exhibited a high-level tolerant phenotype to chlorhexidine, following several rounds of in vitro selection, using sub-lethal concentrations of the biocide. This mutant showed altered suceptibility to a panel of clinically important antimicrobial compounds. Here we describe a genomic, transcriptomic, proteomic, and phenotypic analysis of the chlorhexidine tolerant S. Typhimurium compared with its isogenic sensitive progenitor. Results from this study describe a chlorhexidine defense network that functions in both the reference chlorhexidine sensitive isolate and the tolerant mutant. The defense network involved multiple cell targets including those associated with the synthesis and modification of the cell wall, the SOS response, virulence, and a shift in cellular metabolism toward anoxic pathways, some of which were regulated by CreB and Fur. In addition, results indicated that chlorhexidine tolerance was associated with more extensive modifications of the same cellular processes involved in this proposed network, as well as a divergent defense response involving the up-regulation of additional targets such as the flagellar apparatus and an altered cellular phosphate metabolism. These data show that sub-lethal concentrations of chlorhexidine induce distinct changes in exposed Salmonella, and our findings provide insights into the mechanisms of action and tolerance to this biocidal agent.
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Affiliation(s)
- Orla Condell
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin Belfield, Dublin, Ireland ; European Program for Public Health Microbiology Training, European Centre for Disease Prevention and Control Stockholm, Sweden
| | - Karen A Power
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin Belfield, Dublin, Ireland
| | - Kristian Händler
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin Dublin, Ireland
| | - Sarah Finn
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin Belfield, Dublin, Ireland
| | - Aine Sheridan
- Food Safety Department, Teagasc Food Research Centre Ashtown, Dublin, Ireland
| | - Kjell Sergeant
- Department of Environment and Agrobiotechnologies (EVA), Centre de Recherche Public-Gabriel Lippmann Belvaux, Luxembourg
| | - Jenny Renaut
- Department of Environment and Agrobiotechnologies (EVA), Centre de Recherche Public-Gabriel Lippmann Belvaux, Luxembourg
| | - Catherine M Burgess
- Food Safety Department, Teagasc Food Research Centre Ashtown, Dublin, Ireland
| | - Jay C D Hinton
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin Dublin, Ireland ; Institute of Integrative Biology, University of Liverpool Liverpool, UK
| | - Jarlath E Nally
- School of Veterinary Medicine, University College Dublin Belfield, Dublin, Ireland
| | - Séamus Fanning
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin Belfield, Dublin, Ireland ; Institute for Global Food Security, Queen's University Belfast Belfast, Northern Ireland
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40
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Kröger C, Colgan A, Srikumar S, Händler K, Sivasankaran SK, Hammarlöf DL, Canals R, Grissom JE, Conway T, Hokamp K, Hinton JCD. An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium. Cell Host Microbe 2014; 14:683-95. [PMID: 24331466 DOI: 10.1016/j.chom.2013.11.010] [Citation(s) in RCA: 333] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 11/13/2013] [Accepted: 11/21/2013] [Indexed: 11/15/2022]
Abstract
Bacterial transcriptional networks consist of hundreds of transcription factors and thousands of promoters. However, the true complexity of transcription in a bacterial pathogen and the effect of the environments encountered during infection remain to be established. We present a simplified approach for global promoter identification in bacteria using RNA-seq-based transcriptomic analyses of 22 distinct infection-relevant environmental conditions. Individual RNA samples were combined to identify most of the 3,838 Salmonella enterica serovar Typhimurium promoters in just two RNA-seq runs. Individual in vitro conditions stimulated characteristic transcriptional signatures, and the suite of 22 conditions induced transcription of 86% of all S. Typhimurium genes. We highlight the environmental conditions that induce the Salmonella pathogenicity islands and present a small RNA expression landscape of 280 sRNAs. This publicly available compendium of environmentally controlled expression of every transcriptional feature of S. Typhimurium constitutes a useful resource for the bacterial research community.
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Affiliation(s)
- Carsten Kröger
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Aoife Colgan
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Shabarinath Srikumar
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Kristian Händler
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Sathesh K Sivasankaran
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Disa L Hammarlöf
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Rocío Canals
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Joe E Grissom
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Tyrrell Conway
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Karsten Hokamp
- Department of Genetics, School of Genetics & Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Jay C D Hinton
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland; Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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41
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Kröger C, Dillon SC, Cameron ADS, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, Hébrard M, Händler K, Colgan A, Leekitcharoenphon P, Langridge GC, Lohan AJ, Loftus B, Lucchini S, Ussery DW, Dorman CJ, Thomson NR, Vogel J, Hinton JCD. The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc Natl Acad Sci U S A 2012; 109:E1277-86. [PMID: 22538806 PMCID: PMC3356629 DOI: 10.1073/pnas.1201061109] [Citation(s) in RCA: 301] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
More than 50 y of research have provided great insight into the physiology, metabolism, and molecular biology of Salmonella enterica serovar Typhimurium (S. Typhimurium), but important gaps in our knowledge remain. It is clear that a precise choreography of gene expression is required for Salmonella infection, but basic genetic information such as the global locations of transcription start sites (TSSs) has been lacking. We combined three RNA-sequencing techniques and two sequencing platforms to generate a robust picture of transcription in S. Typhimurium. Differential RNA sequencing identified 1,873 TSSs on the chromosome of S. Typhimurium SL1344 and 13% of these TSSs initiated antisense transcripts. Unique findings include the TSSs of the virulence regulators phoP, slyA, and invF. Chromatin immunoprecipitation revealed that RNA polymerase was bound to 70% of the TSSs, and two-thirds of these TSSs were associated with σ(70) (including phoP, slyA, and invF) from which we identified the -10 and -35 motifs of σ(70)-dependent S. Typhimurium gene promoters. Overall, we corrected the location of important genes and discovered 18 times more promoters than identified previously. S. Typhimurium expresses 140 small regulatory RNAs (sRNAs) at early stationary phase, including 60 newly identified sRNAs. Almost half of the experimentally verified sRNAs were found to be unique to the Salmonella genus, and <20% were found throughout the Enterobacteriaceae. This description of the transcriptional map of SL1344 advances our understanding of S. Typhimurium, arguably the most important bacterial infection model.
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Affiliation(s)
- Carsten Kröger
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, and
| | - Shane C. Dillon
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, and
| | - Andrew D. S. Cameron
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, and
| | - Kai Papenfort
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Sathesh K. Sivasankaran
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, and
| | - Karsten Hokamp
- Department of Genetics, School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Yanjie Chao
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Alexandra Sittka
- Molecular Pulmonology, Universities of Giessen and Marburg Lung Center, German Center for Lung Research, Philipps University, 35043 Marburg, Germany
| | - Magali Hébrard
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, and
| | - Kristian Händler
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, and
| | - Aoife Colgan
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, and
| | - Pimlapas Leekitcharoenphon
- Department of Systems Biology, Center for Biological Sequence Analysis, and
- National Food Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Gemma C. Langridge
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Amanda J. Lohan
- School of Medicine and Medical Science, Conway Institute, University College Dublin, Dublin 4, Ireland; and
| | - Brendan Loftus
- School of Medicine and Medical Science, Conway Institute, University College Dublin, Dublin 4, Ireland; and
| | - Sacha Lucchini
- Institute of Food Research, Colney, Norwich NR4 7UA, United Kingdom
| | - David W. Ussery
- Department of Systems Biology, Center for Biological Sequence Analysis, and
| | - Charles J. Dorman
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, and
| | - Nicholas R. Thomson
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Jay C. D. Hinton
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, and
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Abstract
The combination of genomics and high-throughput cDNA sequencing technologies has facilitated the identification of many small RNAs (sRNAs) that play a central role in the post-transcriptional gene regulation of Salmonella enterica serovar Typhimurium. To date, most of the functionally characterized sRNAs have been involved in the regulation of processes which are not directly linked to virulence. Just five sRNAs have been found to affect the ability of Salmonella to replicate within mammalian cells, but the precise regulatory mechanisms that are used by sRNAs to control Salmonella pathogenicity at the post-transcriptional level remain to be identified. It is anticipated that an improved understanding of sRNA biology will shed new light on the virulence of Salmonella.
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Affiliation(s)
- Magali Hébrard
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
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Hébrard M, Kröger C, Sivasankaran SK, Händler K, Hinton JCD. The challenge of relating gene expression to the virulence of Salmonella enterica serovar Typhimurium. Curr Opin Biotechnol 2011; 22:200-10. [PMID: 21388802 DOI: 10.1016/j.copbio.2011.02.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 02/04/2011] [Accepted: 02/10/2011] [Indexed: 12/15/2022]
Abstract
The first decade of transcriptomic studies of Salmonella enterica serovar Typhimurium focused upon gene expression in vitro, and during the infection of mammalian cells. The published regulons and stimulons show that the three Type Three Secretion Systems of S. Typhimurium respond to a diverse range of environmental conditions, and are controlled by a hierarchy of regulatory proteins. The integration of in vitro generated transcriptomic data with global gene expression of S. Typhimurium during infection is beginning to yield valuable information. The coordinated regulation of Salmonella gene expression is a key process for survival, adaptation and virulence capacities of the pathogen.
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Affiliation(s)
- Magali Hébrard
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics & Microbiology, Trinity College, Dublin 2, Ireland
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