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Merkt S, Ali S, Gudina EK, Adissu W, Gize A, Muenchhoff M, Graf A, Krebs S, Elsbernd K, Kisch R, Betizazu SS, Fantahun B, Bekele D, Rubio-Acero R, Gashaw M, Girma E, Yilma D, Zeynudin A, Paunovic I, Hoelscher M, Blum H, Hasenauer J, Kroidl A, Wieser A. Long-term monitoring of SARS-CoV-2 seroprevalence and variants in Ethiopia provides prediction for immunity and cross-immunity. Nat Commun 2024; 15:3463. [PMID: 38658564 PMCID: PMC11043357 DOI: 10.1038/s41467-024-47556-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
Under-reporting of COVID-19 and the limited information about circulating SARS-CoV-2 variants remain major challenges for many African countries. We analyzed SARS-CoV-2 infection dynamics in Addis Ababa and Jimma, Ethiopia, focusing on reinfection, immunity, and vaccination effects. We conducted an antibody serology study spanning August 2020 to July 2022 with five rounds of data collection across a population of 4723, sequenced PCR-test positive samples, used available test positivity rates, and constructed two mathematical models integrating this data. A multivariant model explores variant dynamics identifying wildtype, alpha, delta, and omicron BA.4/5 as key variants in the study population, and cross-immunity between variants, revealing risk reductions between 24% and 69%. An antibody-level model predicts slow decay leading to sustained high antibody levels. Retrospectively, increased early vaccination might have substantially reduced infections during the delta and omicron waves in the considered group of individuals, though further vaccination now seems less impactful.
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Affiliation(s)
- Simon Merkt
- Life and Medical Sciences (LIMES), University of Bonn, Bonn, Germany
| | - Solomon Ali
- Saint Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Esayas Kebede Gudina
- Jimma University Clinical Trial Unit, Jimma University Institute of Health, Jimma, Ethiopia
| | - Wondimagegn Adissu
- Jimma University Clinical Trial Unit, Jimma University Institute of Health, Jimma, Ethiopia
| | - Addisu Gize
- Saint Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
- CIH LMU Center for International Health, LMU Munich, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Kira Elsbernd
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
- Institute for Medical Information Processing, Biometry and Epidemiology (IBE), Faculty of Medicine, LMU Munich, Munich, Germany
| | - Rebecca Kisch
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
| | | | - Bereket Fantahun
- Saint Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Delayehu Bekele
- Saint Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Raquel Rubio-Acero
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
| | - Mulatu Gashaw
- Jimma University Clinical Trial Unit, Jimma University Institute of Health, Jimma, Ethiopia
| | - Eyob Girma
- Jimma University Clinical Trial Unit, Jimma University Institute of Health, Jimma, Ethiopia
| | - Daniel Yilma
- Jimma University Clinical Trial Unit, Jimma University Institute of Health, Jimma, Ethiopia
| | - Ahmed Zeynudin
- Jimma University Clinical Trial Unit, Jimma University Institute of Health, Jimma, Ethiopia
| | - Ivana Paunovic
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
- Immunology, Infection and Pandemic Research IIP, Fraunhofer ITMP, Munich, Germany
| | - Michael Hoelscher
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
- Immunology, Infection and Pandemic Research IIP, Fraunhofer ITMP, Munich, Germany
- Unit Global Health, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Jan Hasenauer
- Life and Medical Sciences (LIMES), University of Bonn, Bonn, Germany.
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
- Center for Mathematics, Technische Universität München, Garching, Germany.
| | - Arne Kroidl
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany.
| | - Andreas Wieser
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany.
- Immunology, Infection and Pandemic Research IIP, Fraunhofer ITMP, Munich, Germany.
- Faculty of Medicine, Max Von Pettenkofer Institute, LMU Munich, Munich, Germany.
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2
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Esser E, Schulte EC, Graf A, Karollus A, Smith NH, Michler T, Dvoretskii S, Angelov A, Sonnabend M, Peter S, Engesser C, Radonic A, Thürmer A, von Kleist M, Gebhardt F, da Costa CP, Busch DH, Muenchhoff M, Blum H, Keppler OT, Gagneur J, Protzer U. Viral genome sequencing to decipher in-hospital SARS-CoV-2 transmission events. Sci Rep 2024; 14:5768. [PMID: 38459123 PMCID: PMC10923895 DOI: 10.1038/s41598-024-56162-7] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 03/02/2024] [Indexed: 03/10/2024] Open
Abstract
The SARS-CoV-2 pandemic has highlighted the need to better define in-hospital transmissions, a need that extends to all other common infectious diseases encountered in clinical settings. To evaluate how whole viral genome sequencing can contribute to deciphering nosocomial SARS-CoV-2 transmission 926 SARS-CoV-2 viral genomes from 622 staff members and patients were collected between February 2020 and January 2021 at a university hospital in Munich, Germany, and analysed along with the place of work, duration of hospital stay, and ward transfers. Bioinformatically defined transmission clusters inferred from viral genome sequencing were compared to those inferred from interview-based contact tracing. An additional dataset collected at the same time at another university hospital in the same city was used to account for multiple independent introductions. Clustering analysis of 619 viral genomes generated 19 clusters ranging from 3 to 31 individuals. Sequencing-based transmission clusters showed little overlap with those based on contact tracing data. The viral genomes were significantly more closely related to each other than comparable genomes collected simultaneously at other hospitals in the same city (n = 829), suggesting nosocomial transmission. Longitudinal sampling from individual patients suggested possible cross-infection events during the hospital stay in 19.2% of individuals (14 of 73 individuals). Clustering analysis of SARS-CoV-2 whole genome sequences can reveal cryptic transmission events missed by classical, interview-based contact tracing, helping to decipher in-hospital transmissions. These results, in line with other studies, advocate for viral genome sequencing as a pathogen transmission surveillance tool in hospitals.
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Affiliation(s)
- Elisabeth Esser
- Institute of Virology, School of Medicine & Health, Technical University of Munich/Helmholtz Munich, Munich, Germany
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Eva C Schulte
- Institute of Virology, School of Medicine & Health, Technical University of Munich/Helmholtz Munich, Munich, Germany
- Department of Psychiatry, University Hospital, LMU Munich, Munich, Germany
- Institute of Psychiatric Phenomics and Genomics, University Hospital, LMU Munich, Munich, Germany
- Department of Psychiatry, University Hospital, Medical Faculty, University of Bonn, Bonn, Germany
- Institute of Human Genetics, University Hospital, Medical Faculty, University of Bonn, Bonn, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Alexander Karollus
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Nicholas H Smith
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Thomas Michler
- Institute of Virology, School of Medicine & Health, Technical University of Munich/Helmholtz Munich, Munich, Germany
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Stefan Dvoretskii
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Angel Angelov
- NGS Competence Center, University of Tübingen, Tübingen, Germany
| | | | - Silke Peter
- NGS Competence Center, University of Tübingen, Tübingen, Germany
| | | | - Aleksandar Radonic
- Method development, Research Infrastructure & IT (MFI), Robert-Koch Institute (RKI), Berlin, Germany
| | - Andrea Thürmer
- Method development, Research Infrastructure & IT (MFI), Robert-Koch Institute (RKI), Berlin, Germany
| | - Max von Kleist
- Department of Mathematics and Computer Science, Freie Universität (FU) Berlin, Berlin, Germany
- Project Groups, Robert-Koch Institute (RKI), Berlin, Germany
| | - Friedemann Gebhardt
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, Munich, Germany
| | - Clarissa Prazeres da Costa
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Maximilian Muenchhoff
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Oliver T Keppler
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- Institute of Human Genetics, School of Medicine & Health, Technical University of Munich, Munich, Germany.
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany.
| | - Ulrike Protzer
- Institute of Virology, School of Medicine & Health, Technical University of Munich/Helmholtz Munich, Munich, Germany.
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany.
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3
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Chang Y, Bach L, Hasiuk M, Wen L, Elmzzahi T, Tsui C, Gutiérrez-Melo N, Steffen T, Utzschneider DT, Raj T, Jost PJ, Heink S, Cheng J, Burton OT, Zeiträg J, Alterauge D, Dahlström F, Becker JC, Kastl M, Symeonidis K, van Uelft M, Becker M, Reschke S, Krebs S, Blum H, Abdullah Z, Paeschke K, Ohnmacht C, Neumann C, Liston A, Meissner F, Korn T, Hasenauer J, Heissmeyer V, Beyer M, Kallies A, Jeker LT, Baumjohann D. TGF-β specifies T FH versus T H17 cell fates in murine CD4 + T cells through c-Maf. Sci Immunol 2024; 9:eadd4818. [PMID: 38427718 DOI: 10.1126/sciimmunol.add4818] [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: 06/14/2022] [Accepted: 01/05/2024] [Indexed: 03/03/2024]
Abstract
T follicular helper (TFH) cells are essential for effective antibody responses, but deciphering the intrinsic wiring of mouse TFH cells has long been hampered by the lack of a reliable protocol for their generation in vitro. We report that transforming growth factor-β (TGF-β) induces robust expression of TFH hallmark molecules CXCR5 and Bcl6 in activated mouse CD4+ T cells in vitro. TGF-β-induced mouse CXCR5+ TFH cells are phenotypically, transcriptionally, and functionally similar to in vivo-generated TFH cells and provide critical help to B cells. The study further reveals that TGF-β-induced CXCR5 expression is independent of Bcl6 but requires the transcription factor c-Maf. Classical TGF-β-containing T helper 17 (TH17)-inducing conditions also yield separate CXCR5+ and IL-17A-producing cells, highlighting shared and distinct cell fate trajectories of TFH and TH17 cells. We demonstrate that excess IL-2 in high-density T cell cultures interferes with the TGF-β-induced TFH cell program, that TFH and TH17 cells share a common developmental stage, and that c-Maf acts as a switch factor for TFH versus TH17 cell fates in TGF-β-rich environments in vitro and in vivo.
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Affiliation(s)
- Yinshui Chang
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
- Institute for Immunology, Faculty of Medicine, Biomedical Center, LMU Munich, Grosshaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Luisa Bach
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Marko Hasiuk
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, Petersgraben 4, CH-4031 Basel, Switzerland
| | - Lifen Wen
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Tarek Elmzzahi
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
- Immunogenomics and Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Carlson Tsui
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Nicolás Gutiérrez-Melo
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Teresa Steffen
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Daniel T Utzschneider
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Timsse Raj
- Institute for Immunology, Faculty of Medicine, Biomedical Center, LMU Munich, Grosshaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Paul Jonas Jost
- Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
| | - Sylvia Heink
- Institute for Experimental Neuroimmunology, Technical University of Munich School of Medicine, 81675 Munich, Germany
| | - Jingyuan Cheng
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Oliver T Burton
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Julia Zeiträg
- Institute for Immunology, Faculty of Medicine, Biomedical Center, LMU Munich, Grosshaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Dominik Alterauge
- Institute for Immunology, Faculty of Medicine, Biomedical Center, LMU Munich, Grosshaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Frank Dahlström
- Institute for Immunology, Faculty of Medicine, Biomedical Center, LMU Munich, Grosshaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Jennifer-Christin Becker
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Melanie Kastl
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Konstantinos Symeonidis
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Martina van Uelft
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - 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
| | - Sarah Reschke
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Zeinab Abdullah
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Katrin Paeschke
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Caspar Ohnmacht
- Center of Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Munich, Germany
| | - Christian Neumann
- Department of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Adrian Liston
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Felix Meissner
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Systems Immunology and Proteomics, Institute of Innate Immunity, Medical Faculty, University of Bonn, Germany
| | - Thomas Korn
- Institute for Experimental Neuroimmunology, Technical University of Munich School of Medicine, 81675 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | - Jan Hasenauer
- Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
- Center for Mathematics, Technical University of Munich, Garching, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Vigo Heissmeyer
- Institute for Immunology, Faculty of Medicine, Biomedical Center, LMU Munich, Grosshaderner Str. 9, 82152 Planegg-Martinsried, Germany
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Feodor-Lynen-Str. 21, 81377 Munich, Germany
| | - Marc Beyer
- Immunogenomics and Neurodegeneration, 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
| | - Axel Kallies
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Lukas T Jeker
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, Petersgraben 4, CH-4031 Basel, Switzerland
| | - Dirk Baumjohann
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
- Institute for Immunology, Faculty of Medicine, Biomedical Center, LMU Munich, Grosshaderner Str. 9, 82152 Planegg-Martinsried, Germany
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4
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Mühlhofer M, Offensperger F, Reschke S, Wallmann G, Csaba G, Berchtold E, Riedl M, Blum H, Haslbeck M, Zimmer R, Buchner J. Deletion of the transcription factors Hsf1, Msn2 and Msn4 in yeast uncovers transcriptional reprogramming in response to proteotoxic stress. FEBS Lett 2024; 598:635-657. [PMID: 38366111 DOI: 10.1002/1873-3468.14821] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024]
Abstract
The response to proteotoxic stresses such as heat shock allows organisms to maintain protein homeostasis under changing environmental conditions. We asked what happens if an organism can no longer react to cytosolic proteotoxic stress. To test this, we deleted or depleted, either individually or in combination, the stress-responsive transcription factors Msn2, Msn4, and Hsf1 in Saccharomyces cerevisiae. Our study reveals a combination of survival strategies, which together protect essential proteins. Msn2 and 4 broadly reprogram transcription, triggering the response to oxidative stress, as well as biosynthesis of the protective sugar trehalose and glycolytic enzymes, while Hsf1 mainly induces the synthesis of molecular chaperones and reverses the transcriptional response upon prolonged mild heat stress (adaptation).
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Affiliation(s)
- Moritz Mühlhofer
- Center for Protein Assemblies, Department of Bioscience, Technische Universität München, Garching, Germany
| | - Felix Offensperger
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Sarah Reschke
- Laboratory for Functional Genome Analysis at the Gene Center, LMU München, München, Germany
| | - Georg Wallmann
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Gergely Csaba
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Evi Berchtold
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Maximilian Riedl
- Center for Protein Assemblies, Department of Bioscience, Technische Universität München, Garching, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis at the Gene Center, LMU München, München, Germany
| | - Martin Haslbeck
- Center for Protein Assemblies, Department of Bioscience, Technische Universität München, Garching, Germany
| | - Ralf Zimmer
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Johannes Buchner
- Center for Protein Assemblies, Department of Bioscience, Technische Universität München, Garching, Germany
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5
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Wilhelm A, Schoth J, Meinert-Berning C, Bastian D, Blum H, Elsinga G, Graf A, Heijnen L, Ho J, Kluge M, Krebs S, Stange C, Uchaikina A, Dolny R, Wurzbacher C, Drewes JE, Medema G, Tiehm A, Ciesek S, Teichgräber B, Wintgens T, Weber FA, Widera M. Interlaboratory comparison using inactivated SARS-CoV-2 variants as a feasible tool for quality control in COVID-19 wastewater monitoring. Sci Total Environ 2023; 903:166540. [PMID: 37634730 DOI: 10.1016/j.scitotenv.2023.166540] [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] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/11/2023] [Accepted: 08/22/2023] [Indexed: 08/29/2023]
Abstract
Wastewater-based SARS-CoV-2 epidemiology (WBE) has proven as an excellent tool to monitor pandemic dynamics supporting individual testing strategies. WBE can also be used as an early warning system for monitoring the emergence of novel pathogens or viral variants. However, for a timely transmission of results, sophisticated sample logistics and analytics performed in decentralized laboratories close to the sampling sites are required. Since multiple decentralized laboratories commonly use custom in-house workflows for sample purification and PCR-analysis, comparative quality control of the analytical procedures is essential to report reliable and comparable results. In this study, we performed an interlaboratory comparison at laboratories specialized for PCR and high-throughput-sequencing (HTS)-based WBE analysis. Frozen reserve samples from low COVID-19 incidence periods were spiked with different inactivated authentic SARS-CoV-2 variants in graduated concentrations and ratios. Samples were sent to the participating laboratories for analysis using laboratory specific methods and the reported viral genome copy numbers and the detection of viral variants were compared with the expected values. All PCR-laboratories reported SARS-CoV-2 genome copy equivalents (GCE) for all spiked samples with a mean intra- and inter-laboratory variability of 19 % and 104 %, respectively, largely reproducing the spike-in scheme. PCR-based genotyping was, in dependence of the underlying PCR-assay performance, able to predict the relative amount of variant specific substitutions even in samples with low spike-in amount. The identification of variants by HTS, however, required >100 copies/ml wastewater and had limited predictive value when analyzing at a genome coverage below 60 %. This interlaboratory test demonstrates that despite highly heterogeneous isolation and analysis procedures, overall SARS-CoV-2 GCE and mutations were determined accurately. Hence, decentralized SARS-CoV-2 wastewater monitoring is feasible to generate comparable analysis results. However, since not all assays detected the correct variant, prior evaluation of PCR and sequencing workflows as well as sustained quality control such as interlaboratory comparisons are mandatory for correct variant detection.
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Affiliation(s)
- Alexander Wilhelm
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany
| | - Jens Schoth
- Emschergenossenschaft/Lippeverband, Kronprinzenstraße 24, D-45128 Essen, Germany
| | | | - Daniel Bastian
- FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University, Kackertstraße 15-17, D-52056 Aachen, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Feodor-Lynen-Straße 25, D-81377 Munich, Germany
| | - Goffe Elsinga
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Feodor-Lynen-Straße 25, D-81377 Munich, Germany
| | - Leo Heijnen
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Johannes Ho
- TZW: DVGW-Technologiezentrum Wasser, Karlsruher Str. 84, 76139 Karlsruhe, Germany
| | - Mariana Kluge
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Feodor-Lynen-Straße 25, D-81377 Munich, Germany
| | - Claudia Stange
- TZW: DVGW-Technologiezentrum Wasser, Karlsruher Str. 84, 76139 Karlsruhe, Germany
| | - Anna Uchaikina
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany
| | - Regina Dolny
- Institute of Environmental Engineering, RWTH Aachen University, Mies-van-der-Rohe-Strasse 1, D-52074 Aachen, Germany
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany
| | - Jörg E Drewes
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany
| | - Gertjan Medema
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Andreas Tiehm
- TZW: DVGW-Technologiezentrum Wasser, Karlsruher Str. 84, 76139 Karlsruhe, Germany
| | - Sandra Ciesek
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany; German Center for Infection Research (DZIF), 38124 Braunschweig, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, D 60595 Frankfurt am Main, Germany
| | - Burkhard Teichgräber
- Emschergenossenschaft/Lippeverband, Kronprinzenstraße 24, D-45128 Essen, Germany
| | - Thomas Wintgens
- Institute of Environmental Engineering, RWTH Aachen University, Mies-van-der-Rohe-Strasse 1, D-52074 Aachen, Germany
| | - Frank-Andreas Weber
- FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University, Kackertstraße 15-17, D-52056 Aachen, Germany
| | - Marek Widera
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany.
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6
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Moosburner M, Alibegovic L, Hasselmann K, Gaiderov A, Hildebrand J, Philippou-Massier J, Blum H, Fischer L, Dreyling M, Silkenstedt E. Combined treatment with crizotinib and temsirolimus is an effective strategy in mantle cell lymphoma and can overcome acquired resistance to temsirolimus. Hematol Oncol 2023; 41:858-868. [PMID: 37300279 DOI: 10.1002/hon.3194] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/12/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023]
Abstract
Constitutive activation of the PI3K/AKT/mTOR-pathway plays an important role in the pathogenesis of mantle cell lymphoma (MCL), leading to approval of the mTOR inhibitor temsirolimus for relapsed or refractory MCL. Yet, despite favorable initial response rates, early relapses under treatment have been observed. Therefore, understanding the underlying mechanisms of temsirolimus resistance and developing strategies to overcome it is highly warranted. Here, we established a new temsirolimus-resistant MCL cell line to evaluate the molecular background of resistance to this drug. Transcriptome profiling and gene set enrichment analysis comparing temsirolimus-sensitive and -resistant cell lines showed significant upregulation of PI3K/AKT/mTor-, RAS signaling- and the RTK-dependent PDGFR-, FGFR-, Met- and ALK-signaling-pathways in the resistant cells. Furthermore, MET, known as important proto-oncogene and mediator of drug resistance, was among the most upregulated genes in the resistant cells. Importantly, Met protein was overexpressed in both, MCL cells with acquired as well as intrinsic temsirolimus resistance, but could not be detected in any of the temsirolimus sensitive ones. Combined pharmacological inhibition of mTOR and Met signaling with temsirolimus and the RTK inhibitor crizotinib significantly restored sensitivity to temsirolimus. Furthermore, this combined treatment proved to be synergistic in all MCL cell lines investigated and was also active in primary MCL cells. In summary, we showed for the first time that overexpression of MET plays an important role for mediating temsirolimus resistance in MCL and combined treatment with temsirolimus and crizotinib is a very promising therapeutic approach for MCL and an effective strategy to overcome temsirolimus resistance.
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Affiliation(s)
- Marie Moosburner
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University, Munich, Germany
| | - Lamija Alibegovic
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University, Munich, Germany
| | - Korbinian Hasselmann
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University, Munich, Germany
| | - Anton Gaiderov
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University, Munich, Germany
| | - Johannes Hildebrand
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University, Munich, Germany
| | - Julia Philippou-Massier
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, University of Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, University of Munich, Munich, Germany
| | - Luca Fischer
- Department of Medicine III, LMU University Hospital Großhadern of the Ludwig-Maximilians-University, Munich, Germany
| | - Martin Dreyling
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University, Munich, Germany
- Department of Medicine III, LMU University Hospital Großhadern of the Ludwig-Maximilians-University, Munich, Germany
| | - Elisabeth Silkenstedt
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians-University, Munich, Germany
- Department of Medicine III, LMU University Hospital Großhadern of the Ludwig-Maximilians-University, Munich, Germany
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7
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Glueck OM, Liang X, Badell I, Wratil PR, Graf A, Krebs S, Blum H, Hellmuth JC, Scherer C, Hollaus A, Spaeth PM, Karakoc B, Fuchs T, Zimmermann J, Kauke T, Moosmann A, Keppler OT, Schneider C, Muenchhoff M. Impaired immune responses and prolonged viral replication in lung allograft recipients infected with SARS-CoV-2 in the early phase after transplantation. Infection 2023:10.1007/s15010-023-02116-6. [PMID: 37922037 DOI: 10.1007/s15010-023-02116-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/12/2023] [Indexed: 11/05/2023]
Abstract
PURPOSE Lung transplant recipients are at increased risk of severe disease following infection with severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) due to high-dose immunosuppressive drugs and the lung is the main organ affected by Coronavirus disease 2019 (COVID-19). Several studies have confirmed increased SARS-CoV-2-related mortality and morbidity in patients living with lung allografts; however, detailed immunological studies of patients with SARS-CoV-2 infection in the early phase following transplantation remain scarce. METHODS We investigated patients who were infected with SARS-CoV-2 in the early phase (18-103 days) after receiving double-lung allografts (n = 4, LuTx) in comparison to immunocompetent patients who had not received solid organ transplants (n = 88, noTx). We analyzed SARS-CoV-2-specific antibody responses against the SARS-CoV-2 spike and nucleocapsid proteins using enzyme-linked immunosorbent assays (ELISA), chemiluminescence immunoassays (CLIA), and immunoblot assays. T cell responses were investigated using Elispot assays. RESULTS One LuTx patient suffered from persistent infection with fatal outcome 122 days post-infection despite multiple interventions including remdesivir, convalescent plasma, and the monoclonal antibody bamlanivimab. Two patients experienced clinically mild disease with prolonged viral shedding (47 and 79 days), and one patient remained asymptomatic. Antibody and T cell responses were significantly reduced or undetectable in all LuTx patients compared to noTx patients. CONCLUSION Patients in the early phase following lung allograft transplantation are vulnerable to infection with SARS-CoV-2 due to impaired immune responses. This patient population should be vaccinated before LuTx, protected from infection post-LuTx, and in case of infection treated generously with currently available interventions.
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Affiliation(s)
- Olaf M Glueck
- Division of Thoracic Surgery, LMU University Hospital, LMU Munich, Munich, Germany
| | - Xiaoling Liang
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Ludwig Maximilian University of Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Irina Badell
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Ludwig Maximilian University of Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Paul R Wratil
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Ludwig Maximilian University of Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilian University of Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilian University of Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilian University of Munich, Munich, Germany
| | - Johannes C Hellmuth
- Department of Medicine III, LMU University Hospital, LMU Munich, Munich, Germany
| | - Clemens Scherer
- Department of Medicine I, LMU University Hospital, LMU Munich, Munich, Germany
| | - Alexandra Hollaus
- Department of Medicine III, LMU University Hospital, LMU Munich, Munich, Germany
- Helmholtz Munich, Munich, Germany
| | - Patricia M Spaeth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Ludwig Maximilian University of Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Burak Karakoc
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Ludwig Maximilian University of Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Thimo Fuchs
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Ludwig Maximilian University of Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Julia Zimmermann
- Division of Thoracic Surgery, LMU University Hospital, LMU Munich, Munich, Germany
| | - Teresa Kauke
- Division of Thoracic Surgery, LMU University Hospital, LMU Munich, Munich, Germany
| | - Andreas Moosmann
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- Department of Medicine III, LMU University Hospital, LMU Munich, Munich, Germany
- Helmholtz Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Oliver T Keppler
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Ludwig Maximilian University of Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Christian Schneider
- Division of Thoracic Surgery, LMU University Hospital, LMU Munich, Munich, Germany
| | - Maximilian Muenchhoff
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Ludwig Maximilian University of Munich, Pettenkoferstr. 9a, 80336, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany.
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8
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Zaderer V, Abd El Halim H, Wyremblewsky AL, Lupoli G, Dächert C, Muenchhoff M, Graf A, Blum H, Lass-Flörl C, Keppler OT, Huber LA, Posch W, Wilflingseder D. Omicron subvariants illustrate reduced respiratory tissue penetration, cell damage and inflammatory responses in human airway epithelia. Front Immunol 2023; 14:1258268. [PMID: 37915577 PMCID: PMC10616953 DOI: 10.3389/fimmu.2023.1258268] [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: 07/13/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023] Open
Abstract
Introduction To explore whether the reported lower pathogenicity in infected individuals of variant of concern (VoC) Omicron and its current subvariants compared to VoC Delta may be related to fundamental differences in the initial virus-tissue interaction, we assessed their ability to penetrate, replicate and cause damage in a human 3D respiratory model. Methods For this, we used TEER measurements, real-time PCR, LDH, cytokine and complex confocal imaging analyses. Results and discussion We observed that Delta readily penetrated deep into the respiratory epithelium and this was associated with major tissue destruction, high LDH activity, high viral loads and pronounced innate immune activation as observed by intrinsic C3 activation and IL-6 release at infection sites. In contrast, Omicron subvariants BA.5, BQ.1.1 and BF7 remained superficially in the mucosal layer resulting merely in outward-directed destruction of cells, maintenance of epithelial integrity, minimal LDH activity and low basolateral release of virus at infection sites, as well as significantly smaller areas of complement activation and lower IL-6 secretion. Interestingly, also within Omicron subvariants differences were observed with newer Omicron subvariants BQ.1.1 and BF.7 illustrating significantly reduced viral loads, IL-6 release and LDH activity compared to BA.5. Our data indicate that earliest interaction events after SARS-CoV-2 transmission may have a role in shaping disease severity.
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Affiliation(s)
- Viktoria Zaderer
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Hussam Abd El Halim
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Anna-Lena Wyremblewsky
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gaia Lupoli
- Virology, Max von Pettenkofer Institute and Gene Center, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Christopher Dächert
- Virology, Max von Pettenkofer Institute and Gene Center, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Maximilian Muenchhoff
- Virology, Max von Pettenkofer Institute and Gene Center, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Oliver T. Keppler
- Virology, Max von Pettenkofer Institute and Gene Center, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Lukas A. Huber
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
- ADSI - Austrian Drug Screening Institute GmbH, Innsbruck, Austria
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Doris Wilflingseder
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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9
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Ullrich S, Leidescher S, Feodorova Y, Thanisch K, Fini JB, Kaspers B, Weber F, Markova B, Führer D, Romitti M, Krebs S, Blum H, Leonhardt H, Costagliola S, Heuer H, Solovei I. The highly and perpetually upregulated thyroglobulin gene is a hallmark of functional thyrocytes. Front Cell Dev Biol 2023; 11:1265407. [PMID: 37860816 PMCID: PMC10582334 DOI: 10.3389/fcell.2023.1265407] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/22/2023] [Indexed: 10/21/2023] Open
Abstract
Abnormalities are indispensable for studying normal biological processes and mechanisms. In the present work, we draw attention to the remarkable phenomenon of a perpetually and robustly upregulated gene, the thyroglobulin gene (Tg). The gene is expressed in the thyroid gland and, as it has been recently demonstrated, forms so-called transcription loops, easily observable by light microscopy. Using this feature, we show that Tg is expressed at a high level from the moment a thyroid cell acquires its identity and both alleles remain highly active over the entire life of the cell, i.e., for months or years depending on the species. We demonstrate that this high upregulation is characteristic of thyroglobulin genes in all major vertebrate groups. We provide evidence that Tg is not influenced by the thyroid hormone status, does not oscillate round the clock and is expressed during both the exocrine and endocrine phases of thyrocyte activity. We conclude that the thyroglobulin gene represents a unique and valuable model to study the maintenance of a high transcriptional upregulation.
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Affiliation(s)
- Simon Ullrich
- Biocenter, Ludwig Maximilians University Munich, Munich, Germany
| | | | - Yana Feodorova
- Biocenter, Ludwig Maximilians University Munich, Munich, Germany
| | | | - Jean-Baptiste Fini
- Département Adaptations du Vivant (AVIV), Physiologie Moléculaire et Adaptation (PhyMA UMR 7221 CNRS), Muséum National d’Histoire Naturelle, CNRS, CP 32, Paris, France
| | - Bernd Kaspers
- Department for Veterinary Sciences, Ludwig Maximilians University Munich, Planegg, Germany
| | - Frank Weber
- Department of General, Visceral and Transplantation Surgery, Section of Endocrine Surgery, University Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Boyka Markova
- Department of Endocrinology, Diabetes and Metabolism, University Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Dagmar Führer
- Department of Endocrinology, Diabetes and Metabolism, University Duisburg-Essen, University Hospital Essen, Essen, Germany
| | | | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig Maximilians University Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig Maximilians University Munich, Munich, Germany
| | | | | | - Heike Heuer
- Department of Endocrinology, Diabetes and Metabolism, University Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Irina Solovei
- Biocenter, Ludwig Maximilians University Munich, Munich, Germany
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10
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Swoboda AS, Arfelli VC, Danese A, Windisch R, Kerbs P, Redondo Monte E, Bagnoli JW, Chen-Wichmann L, Caroleo A, Cusan M, Krebs S, Blum H, Sterr M, Enard W, Herold T, Colomé-Tatché M, Wichmann C, Greif PA. CSF3R T618I Collaborates With RUNX1-RUNX1T1 to Expand Hematopoietic Progenitors and Sensitizes to GLI Inhibition. Hemasphere 2023; 7:e958. [PMID: 37841755 PMCID: PMC10569757 DOI: 10.1097/hs9.0000000000000958] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/17/2022] [Accepted: 08/22/2023] [Indexed: 10/17/2023] Open
Abstract
Activating colony-stimulating factor-3 receptor gene (CSF3R) mutations are recurrent in acute myeloid leukemia (AML) with t(8;21) translocation. However, the nature of oncogenic collaboration between alterations of CSF3R and the t(8;21) associated RUNX1-RUNX1T1 fusion remains unclear. In CD34+ hematopoietic stem and progenitor cells from healthy donors, double oncogene expression led to a clonal advantage, increased self-renewal potential, and blast-like morphology and distinct immunophenotype. Gene expression profiling revealed hedgehog signaling as a potential mechanism, with upregulation of GLI2 constituting a putative pharmacological target. Both primary hematopoietic cells and the t(8;21) positive AML cell line SKNO-1 showed increased sensitivity to the GLI inhibitor GANT61 when expressing CSF3R T618I. Our findings suggest that during leukemogenesis, the RUNX1-RUNXT1 fusion and CSF3R mutation act in a synergistic manner to alter hedgehog signaling, which can be exploited therapeutically.
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Affiliation(s)
- Anja S. Swoboda
- Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vanessa C. Arfelli
- Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anna Danese
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
- Department of Physiological Genomics, Biomedical Center Munich, Ludwig-Maximilians University, Germany
| | - Roland Windisch
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, LMU Munich, Germany
| | - Paul Kerbs
- Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Enric Redondo Monte
- Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes W. Bagnoli
- Anthropology and Human Genomics, Faculty of Biology, LMU Munich, Martinsried, Germany
| | - Linping Chen-Wichmann
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, LMU Munich, Germany
| | - Alessandra Caroleo
- Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Monica Cusan
- Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Krebs
- Gene Center - Laboratory for Functional Genome Analysis, LMU Munich, Germany
| | - Helmut Blum
- Gene Center - Laboratory for Functional Genome Analysis, LMU Munich, Germany
| | - Michael Sterr
- Institute of Diabetes and Regeneration Research, Helmholtz Diabetes Center, Helmholtz Center Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, LMU Munich, Martinsried, Germany
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maria Colomé-Tatché
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Christian Wichmann
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, LMU Munich, Germany
| | - Philipp A. Greif
- Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
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11
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Osterman A, Krenn F, Iglhaut M, Badell I, Lehner A, Späth PM, Stern M, Both H, Bender S, Muenchhoff M, Graf A, Krebs S, Blum H, Grimmer T, Durner J, Czibere L, Dächert C, Grzimek-Koschewa N, Protzer U, Kaderali L, Baldauf HM, Keppler OT. Automated antigen assays display a high heterogeneity for the detection of SARS-CoV-2 variants of concern, including several Omicron sublineages. Med Microbiol Immunol 2023; 212:307-322. [PMID: 37561226 PMCID: PMC10501957 DOI: 10.1007/s00430-023-00774-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
Diagnostic tests for direct pathogen detection have been instrumental to contain the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) pandemic. Automated, quantitative, laboratory-based nucleocapsid antigen (Ag) tests for SARS-CoV-2 have been launched alongside nucleic acid-based test systems and point-of-care (POC) lateral-flow Ag tests. Here, we evaluated four commercial Ag tests on automated platforms for the detection of different sublineages of the SARS-CoV-2 Omicron variant of concern (VoC) (B.1.1.529) in comparison with "non-Omicron" VoCs. A total of 203 Omicron PCR-positive respiratory swabs (53 BA.1, 48 BA.2, 23 BQ.1, 39 XBB.1.5 and 40 other subvariants) from the period February to March 2022 and from March 2023 were examined. In addition, tissue culture-expanded clinical isolates of Delta (B.1.617.2), Omicron-BA.1, -BF.7, -BN.1 and -BQ.1 were studied. These results were compared to previously reported data from 107 clinical "non-Omicron" samples from the end of the second pandemic wave (February to March 2021) as well as cell culture-derived samples of wildtype (wt) EU-1 (B.1.177), Alpha VoC (B.1.1.7) and Beta VoC (B.1.351)). All four commercial Ag tests were able to detect at least 90.9% of Omicron-containing samples with high viral loads (Ct < 25). The rates of true-positive test results for BA.1/BA.2-positive samples with intermediate viral loads (Ct 25-30) ranged between 6.7% and 100.0%, while they dropped to 0 to 15.4% for samples with low Ct values (> 30). This heterogeneity was reflected also by the tests' 50%-limit of detection (LoD50) values ranging from 44,444 to 1,866,900 Geq/ml. Respiratory samples containing Omicron-BQ.1/XBB.1.5 or other Omicron subvariants that emerged in 2023 were detected with enormous heterogeneity (0 to 100%) for the intermediate and low viral load ranges with LoD50 values between 23,019 and 1,152,048 Geq/ml. In contrast, detection of "non-Omicron" samples was more sensitive, scoring positive in 35 to 100% for the intermediate and 1.3 to 32.9% of cases for the low viral loads, respectively, corresponding to LoD50 values ranging from 6181 to 749,792 Geq/ml. All four assays detected cell culture-expanded VoCs Alpha, Beta, Delta and Omicron subvariants carrying up to six amino acid mutations in the nucleocapsid protein with sensitivities comparable to the non-VoC EU-1. Overall, automated quantitative SARS-CoV-2 Ag assays are not more sensitive than standard rapid antigen tests used in POC settings and show a high heterogeneity in performance for VoC recognition. The best of these automated Ag tests may have the potential to complement nucleic acid-based assays for SARS-CoV-2 diagnostics in settings not primarily focused on the protection of vulnerable groups. In light of the constant emergence of new Omicron subvariants and recombinants, most recently the XBB lineage, these tests' performance must be regularly re-evaluated, especially when new VoCs carry mutations in the nucleocapsid protein or immunological and clinical parameters change.
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Affiliation(s)
- Andreas Osterman
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Franziska Krenn
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Iglhaut
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Irina Badell
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Andreas Lehner
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia M Späth
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Marcel Stern
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Hanna Both
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Sabine Bender
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID‑19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Timo Grimmer
- Department of Psychiatry and Psychotherapy, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Jürgen Durner
- Labor Becker MVZ GbR, Munich, Germany
- Department of Conservative Dentistry and Periodontology, University Hospital, LMU München, Munich, Germany
| | | | - Christopher Dächert
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Natascha Grzimek-Koschewa
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Ulrike Protzer
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Hanna-Mari Baldauf
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany.
- COVID‑19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany.
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12
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Krenn F, Dächert C, Badell I, Lupoli G, Öztan GN, Feng T, Schneider N, Huber M, Both H, Späth PM, Muenchhoff M, Graf A, Krebs S, Blum H, Durner J, Czibere L, Kaderali L, Keppler OT, Baldauf HM, Osterman A. Ten rapid antigen tests for SARS-CoV-2 widely differ in their ability to detect Omicron-BA.4 and -BA.5. Med Microbiol Immunol 2023; 212:323-337. [PMID: 37561225 PMCID: PMC10501931 DOI: 10.1007/s00430-023-00775-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
Since late 2021, the variant landscape of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been dominated by the variant of concern (VoC) Omicron and its sublineages. We and others have shown that the detection of Omicron-BA.1 and -BA.2-positive respiratory specimens by rapid antigen tests (RATs) is impaired compared to Delta VoC-containing samples. Here, in a single-center retrospective laboratory study, we evaluated the performance of ten most commonly used RATs for the detection of Omicron-BA.4 and -BA.5 infections. We used 171 respiratory swab specimens from SARS-CoV-2 RNA-positive patients, of which 71 were classified as BA.4 and 100 as BA.5. All swabs were collected between July and September 2022. 50 SARS-CoV-2 PCR-negative samples from healthy individuals, collected in October 2022, showed high specificity in 9 out of 10 RATs. When assessing analytical sensitivity using clinical specimens, the 50% limit of detection (LoD50) ranged from 7.6 × 104 to 3.3 × 106 RNA copies subjected to the RATs for BA.4 compared to 6.8 × 104 to 3.0 × 106 for BA.5. Overall, intra-assay differences for the detection of these two Omicron subvariants were not significant for both respiratory swabs and tissue culture-expanded virus isolates. In contrast, marked heterogeneity was observed among the ten RATs: to be positive in these point-of-care tests, up to 443-fold (BA.4) and up to 56-fold (BA.5) higher viral loads were required for the worst performing RAT compared to the best performing RAT. True-positive rates for Omicron-BA.4- or -BA.5-containing specimens in the highest viral load category (Ct values < 25) ranged from 94.3 to 34.3%, dropping to 25.6 to 0% for samples with intermediate Ct values (25-30). We conclude that the high heterogeneity in the performance of commonly used RATs remains a challenge for the general public to obtain reliable results in the evolving Omicron subvariant-driven pandemic.
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Affiliation(s)
- Franziska Krenn
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Christopher Dächert
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Irina Badell
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Gaia Lupoli
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Gamze Naz Öztan
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Tianle Feng
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Nikolas Schneider
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Melanie Huber
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Hanna Both
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia M. Späth
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | | | | | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Oliver T. Keppler
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany
| | - Hanna-Mari Baldauf
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Andreas Osterman
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
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13
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Yahia Y, Pigeot A, El Aabidine AZ, Shah N, Karasu N, Forné I, Krebs S, Blum H, Esnault C, Sexton T, Imhof A, Eick D, Andrau J. RNA polymerase II CTD is dispensable for transcription and required for termination in human cells. EMBO Rep 2023; 24:e56150. [PMID: 37424514 PMCID: PMC10481650 DOI: 10.15252/embr.202256150] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 06/21/2023] [Accepted: 06/27/2023] [Indexed: 07/11/2023] Open
Abstract
The largest subunit of RNA polymerase (Pol) II harbors an evolutionarily conserved C-terminal domain (CTD), composed of heptapeptide repeats, central to the transcriptional process. Here, we analyze the transcriptional phenotypes of a CTD-Δ5 mutant that carries a large CTD truncation in human cells. Our data show that this mutant can transcribe genes in living cells but displays a pervasive phenotype with impaired termination, similar to but more severe than previously characterized mutations of CTD tyrosine residues. The CTD-Δ5 mutant does not interact with the Mediator and Integrator complexes involved in the activation of transcription and processing of RNAs. Examination of long-distance interactions and CTCF-binding patterns in CTD-Δ5 mutant cells reveals no changes in TAD domains or borders. Our data demonstrate that the CTD is largely dispensable for the act of transcription in living cells. We propose a model in which CTD-depleted Pol II has a lower entry rate onto DNA but becomes pervasive once engaged in transcription, resulting in a defect in termination.
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Affiliation(s)
- Yousra Yahia
- Institut de Génétique Moléculaire de Montpellier (IGMM), CNRS‐UMR5535MontpellierFrance
| | - Alexia Pigeot
- Institut de Génétique Moléculaire de Montpellier (IGMM), CNRS‐UMR5535MontpellierFrance
| | - Amal Zine El Aabidine
- Institut de Génétique Moléculaire de Montpellier (IGMM), CNRS‐UMR5535MontpellierFrance
| | - Nilay Shah
- Department of Molecular Epigenetics, Helmholtz Center MunichCenter of Integrated Protein Science MunichMunichGermany
- Present address:
Neuberg Center for Genomic MedicineNeuberg Supratech Reference LaboratoryGujaratIndia
| | - Nezih Karasu
- Institut de Génétique Moléculaire de Montpellier (IGMM), CNRS‐UMR5535MontpellierFrance
- Institute of Genetics and Molecular and Cellular Biology (IGBMC)IllkirchFrance
| | | | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene CenterLudwig‐Maximilians‐UniversitätMunichGermany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene CenterLudwig‐Maximilians‐UniversitätMunichGermany
| | - Cyril Esnault
- Institut de Génétique Moléculaire de Montpellier (IGMM), CNRS‐UMR5535MontpellierFrance
| | - Tom Sexton
- Institute of Genetics and Molecular and Cellular Biology (IGBMC)IllkirchFrance
| | - Axel Imhof
- Biomedical Center Munich, ZFPMartinsriedGermany
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center MunichCenter of Integrated Protein Science MunichMunichGermany
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14
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Rabaglino MB, Forde N, Besenfelder U, Havlicek V, Blum H, Graf A, Wolf E, Lonergan P. Maternal metabolic status and in-vitro culture conditions during embryonic genome activation deregulate the expression of energy-related genes in the bovine 16-cells embryo. PLoS One 2023; 18:e0290689. [PMID: 37624829 PMCID: PMC10456174 DOI: 10.1371/journal.pone.0290689] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
The molecular consequences of the metabolic stress caused by milk production of dairy cows in the early embryo are largely unknown. The objective was to determine the impact of dam metabolic status or in vitro culture during embryonic genome activation (EGA) on the transcriptomic profiles of bovine 16-cell stage embryos. Two days after synchronized oestrus, in vitro produced 2- to 4-cell stage embryos were endoscopically transferred in pools of 50 into the oviduct ipsilateral to the corpus luteum of lactating (LACT, n = 3) or nonlactating (i.e. dried off immediately at calving; DRY, n = 3) dairy cows. On Day 4, the oviducts were flushed to recover the embryos. Pools of five Day-2 embryos (n = 5) and Day-4 16-cell stage embryos obtained in vitro (n = 3) or from LACT or DRY cows were subjected to RNAseq. Temporally differentially expressed genes (DEG; FDR<0.05) between Day-2 and Day-4 embryos were determined considering the differences between the three conditions under which EGA occurred. Also, DEG between Day-4 embryos derived from the three conditions were identified. Functional analysis of the temporal DEG demonstrated that genes involved in ribosome, translation and oxidative phosphorylation in the mitochondria were strongly more expressed in Day-4 than Day-2 embryos. Comparison of Day-4 embryos that underwent EGA in vitro, or in LACT or DRY cows, identified DEG enriching for mitochondrial respiration and protein translation, including the mTOR pathway. In conclusion, exposure of the embryo to an unfavourable maternal metabolic status during EGA influences its transcriptome and potentially the competence for pregnancy establishment.
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Affiliation(s)
- Maria B. Rabaglino
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Niamh Forde
- Division of Reproduction and Early Development, School of Medicine, University of Leeds, Leeds, United Kingdom
| | - Urban Besenfelder
- Reproduction Centre Wieselburg RCW, Institute for Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Vitezslav Havlicek
- Reproduction Centre Wieselburg RCW, Institute for Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU, Munich, Germany
| | - Eckhard Wolf
- Laboratory for Functional Genome Analysis, Gene Center, LMU, Munich, Germany
| | - Patrick Lonergan
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
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15
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Diem G, Dichtl S, Zaderer V, Lass-Flörl C, Reindl M, Lupoli G, Dächert C, Muenchhoff M, Graf A, Blum H, Keppler OT, Wilflingseder D, Posch W. Salivary antibodies induced by BA.4/BA.5-convalescence or bivalent booster Immunoglobulin vaccination protect against novel SARS-COV-2 variants of concern. Microbiol Spectr 2023; 11:e0179323. [PMID: 37551989 PMCID: PMC10581068 DOI: 10.1128/spectrum.01793-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/28/2023] [Indexed: 08/09/2023] Open
Abstract
Currently, SARS-CoV-2 Omicron BA.5 subvariants BF.7 and BQ.1.1 are rapidly emerging worldwide. To evaluate the SARS-CoV-2-neutralizing capacity of sera and saliva from triple vaccinated individuals, either boosted with an adapted bivalent COVID-19 vaccine or recovered from BA.4/BA.5 infection, we analyzed the sensitivity of replication-competent SARS-CoV-2 Omicron subvariants BA.4/5, BQ.1.1 and BF.7 to neutralization. Analysis of SARS-CoV-2-specific IgGs and IgAs showed increased serum IgG titers in the vaccinated group, while the serum and salivary IgA levels were comparable. Similar and efficient serum neutralization against the ancestral strain of SARS-CoV-2 and Omicron BA.4/BA.5 was detected in both cohorts, but critically reduced for BQ.1.1 and BF.7. In contrast, salivary neutralization against BA.4/BA.5 was increased in the convalescent compared to the vaccinated group, while salivary neutralizing capacity against BQ.1.1 and BF.7 was comparable in these groups. Further, personalized protective effects studied in a human 3D respiratory model revealed the importance of salivary protection against different Omicron subvariants. IMPORTANCE In BA.4/BA.5-convalescent versus vaccinated groups, salivary neutralization capacity increased against SARS-CoV-2 Omicron BA.4/BA.5. In contrast, it neutralized novel Omicron subvariants BQ.1.1 and BF.7 similarly. Salivary protection against various Omicron subvariants was even more evident when tested in a personalized approach using highly differentiated respiratory human 3D models.
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Affiliation(s)
- Gabriel Diem
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Stefanie Dichtl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Viktoria Zaderer
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Markus Reindl
- Clinical Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gaia Lupoli
- Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Christopher Dächert
- Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Oliver T. Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Doris Wilflingseder
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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16
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Gong S, Sun N, Meyer LS, Tetti M, Koupourtidou C, Krebs S, Masserdotti G, Blum H, Rainey WE, Reincke M, Walch A, Williams TA. Primary Aldosteronism: Spatial Multiomics Mapping of Genotype-Dependent Heterogeneity and Tumor Expansion of Aldosterone-Producing Adenomas. Hypertension 2023; 80:1555-1567. [PMID: 37125608 PMCID: PMC10330203 DOI: 10.1161/hypertensionaha.123.20921] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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] [Received: 01/10/2023] [Accepted: 04/10/2023] [Indexed: 05/02/2023]
Abstract
BACKGROUND Primary aldosteronism is frequently caused by an adrenocortical aldosterone-producing adenoma (APA) carrying a somatic mutation that drives aldosterone overproduction. APAs with a mutation in KCNJ5 (APA-KCNJ5MUT) are characterized by heterogeneous CYP11B2 (aldosterone synthase) expression, a particular cellular composition and larger tumor diameter than those with wild-type KCNJ5 (APA-KCNJ5WT). We exploited these differences to decipher the roles of transcriptome and metabolome reprogramming in tumor pathogenesis. METHODS Consecutive adrenal cryosections (7 APAs and 7 paired adjacent adrenal cortex) were analyzed by spatial transcriptomics (10x Genomics platform) and metabolomics (in situ matrix-assisted laser desorption/ionization mass spectrometry imaging) co-integrated with CYP11B2 immunohistochemistry. RESULTS We identified intratumoral transcriptional heterogeneity that delineated functionally distinct biological pathways. Common transcriptomic signatures were established across all APA specimens which encompassed 2 distinct transcriptional profiles in CYP11B2-immunopositive regions (CYP11B2-type 1 or 2). The CYP11B2-type 1 signature was characterized by zona glomerulosa gene markers and was detected in both APA-KCNJ5MUT and APA-KCNJ5WT. The CYP11B2-type 2 signature displayed markers of the zona fasciculata or reticularis and predominated in APA-KCNJ5MUT. Metabolites that promote oxidative stress and cell death accumulated in APA-KCNJ5WT. In contrast, antioxidant metabolites were abundant in APA-KCNJ5MUT. Finally, APA-like cell subpopulations-negative for CYP11B2 gene expression-were identified in adrenocortical tissue adjacent to APAs suggesting the existence of tumor precursor states. CONCLUSIONS Our findings provide insight into intra- and intertumoral transcriptional heterogeneity and support a role for prooxidant versus antioxidant systems in APA pathogenesis highlighting genotype-dependent capacities for tumor expansion.
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Affiliation(s)
- Siyuan Gong
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU München, München, Germany
| | - Na Sun
- Research Unit Analytical Pathology, German Research Center for Environmental Health, Helmholtz Zentrum München, Germany
| | - Lucie S Meyer
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU München, München, Germany
| | - Martina Tetti
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU München, München, Germany
| | - Christina Koupourtidou
- Department for Cell Biology and Anatomy, Biomedical Center, Ludwig-Maximilians-Universität (LMU), Planegg-Martinsried, Germany
- Graduate School Systemic Neurosciences, Ludwig-Maximilians-Universität (LMU), Planegg-Martinsried, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, 81377 Munich, Germany
| | - Giacomo Masserdotti
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany
- Physiological Genomics, Biomedical Center (BMC), Ludwig-Maximilians-Universität (LMU), Planegg-Martinsried, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, 81377 Munich, Germany
| | - William E. Rainey
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
- Division of Metabolism, Endocrine, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Martin Reincke
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU München, München, Germany
| | - Axel Walch
- Research Unit Analytical Pathology, German Research Center for Environmental Health, Helmholtz Zentrum München, Germany
| | - Tracy Ann Williams
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU München, München, Germany
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17
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Bunse T, Koerber N, Wintersteller H, Schneider J, Graf A, Radonic A, Thuermer A, von Kleist M, Blum H, Spinner CD, Bauer T, Knolle PA, Protzer U, Schulte EC. T-Cell-Dominated Immune Response Resolves Protracted SARS-CoV-2 Infection in the Absence of Neutralizing Antibodies in an Immunocompromised Individual. Microorganisms 2023; 11:1562. [PMID: 37375064 DOI: 10.3390/microorganisms11061562] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Immunocompromised individuals are at higher risk of developing protracted and severe COVID-19, and understanding individual disease courses and SARS-CoV-2 immune responses in these individuals is of the utmost importance. For more than two years, we followed an immunocompromised individual with a protracted SARS-CoV-2 infection that was eventually cleared in the absence of a humoral neutralizing SARS-CoV-2 antibody response. By conducting an in-depth examination of this individual's immune response and comparing it to a large cohort of convalescents who spontaneously cleared a SARS-CoV-2 infection, we shed light on the interplay between B- and T-cell immunity and how they interact in clearing SARS-CoV-2 infection.
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Affiliation(s)
- Till Bunse
- Institute of Virology, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Institute of Virology, Helmholtz Munich, Trogerstrasse 30, 81675 Munich, Germany
| | - Nina Koerber
- Institute of Virology, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Institute of Virology, Helmholtz Munich, Trogerstrasse 30, 81675 Munich, Germany
| | - Hannah Wintersteller
- Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Jochen Schneider
- Department of Internal Medicine II, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, 81377 Munich, Germany
| | - Aleksandar Radonic
- Method Development, Research Infrastructure & IT (MFI), Robert-Koch Institute (RKI), 13353 Berlin, Germany
| | - Andrea Thuermer
- Method Development, Research Infrastructure & IT (MFI), Robert-Koch Institute (RKI), 13353 Berlin, Germany
| | - Max von Kleist
- Department of Mathematics and Computer Science, Freie Universität (FU) Berlin, 14195 Berlin, Germany
- Project Groups, Robert-Koch Institute (RKI), 13353 Berlin, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, 81377 Munich, Germany
| | - Christoph D Spinner
- Department of Internal Medicine II, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, 81675 Munich, Germany
| | - Tanja Bauer
- Institute of Virology, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Institute of Virology, Helmholtz Munich, Trogerstrasse 30, 81675 Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, 81675 Munich, Germany
| | - Percy A Knolle
- Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, 81675 Munich, Germany
| | - Ulrike Protzer
- Institute of Virology, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Institute of Virology, Helmholtz Munich, Trogerstrasse 30, 81675 Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, 81675 Munich, Germany
| | - Eva C Schulte
- Institute of Virology, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Institute of Virology, Helmholtz Munich, Trogerstrasse 30, 81675 Munich, Germany
- Department of Psychiatry, University Hospital, LMU Munich, 80336 Munich, Germany
- Institute of Psychiatric Phenomics and Genomics, University Hospital, LMU Munich, 80336 Munich, Germany
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18
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Francis WR, Eitel M, Vargas S, Garcia-Escudero CA, Conci N, Deister F, Mah JL, Guiglielmoni N, Krebs S, Blum H, Leys SP, Wörheide G. The genome of the reef-building glass sponge Aphrocallistes vastus provides insights into silica biomineralization. R Soc Open Sci 2023; 10:230423. [PMID: 37351491 PMCID: PMC10282587 DOI: 10.1098/rsos.230423] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
Well-annotated and contiguous genomes are an indispensable resource for understanding the evolution, development, and metabolic capacities of organisms. Sponges, an ecologically important non-bilaterian group of primarily filter-feeding sessile aquatic organisms, are underrepresented with respect to available genomic resources. Here we provide a high-quality and well-annotated genome of Aphrocallistes vastus, a glass sponge (Porifera: Hexactinellida) that forms large reef structures off the coast of British Columbia (Canada). We show that its genome is approximately 80 Mb, small compared to most other metazoans, and contains nearly 2500 nested genes, more than other genomes. Hexactinellida is characterized by a unique skeletal architecture made of amorphous silicon dioxide (SiO2), and we identified 419 differentially expressed genes between the osculum, i.e. the vertical growth zone of the sponge, and the main body. Among the upregulated ones, mineralization-related genes such as glassin, as well as collagens and actins, dominate the expression profile during growth. Silicateins, suggested being involved in silica mineralization, especially in demosponges, were not found at all in the A. vastus genome and suggests that the underlying mechanisms of SiO2 deposition in the Silicea sensu stricto (Hexactinellida + Demospongiae) may not be homologous.
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Affiliation(s)
- Warren R. Francis
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Eitel
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Catalina A. Garcia-Escudero
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicola Conci
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fabian Deister
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jasmine L. Mah
- Department of Biological Sciences, University of Alberta, Edmonton, Canada T6G 2E9
| | - Nadège Guiglielmoni
- Service Evolution Biologique et Ecologie, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sally P. Leys
- Department of Biological Sciences, University of Alberta, Edmonton, Canada T6G 2E9
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB)–Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
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19
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Stanton DL, Graf A, Maia TS, Blum H, Jiang ZC, Hansen PJ. Absence of a Molecular Circadian Clock in the Preimplantation Embryo is a Conserved Characteristic in the Mammal. Reproduction 2023:REP-23-0104. [PMID: 37387479 DOI: 10.1530/rep-23-0104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/30/2023] [Indexed: 07/01/2023]
Abstract
An embryonic circadian clock could conceivably organize cellular and developmental events temporally and in synchrony with other circadian rhythms in the mother. The hypothesis that a functional molecular clock exists in the preimplantation bovine, pig, human and mouse embryo was tested by using publicly available RNAseq datasets to examine developmental changes in expression of the core genes responsible for the circadian clock - CLOCK, ARNTL, PER1, PER2, CRY1, and CRY2. In general, transcript abundance of each gene decreased as development advanced to the blastocyst stage. The most notable exception was for CRY2, where transcript abundance was low and constant from the 2-cell or 4-cell to blastocyst stage. Developmental patterns were generally the same for all species although there were some species-specific patterns such as an absence of PER1 expression in the pig, an increase in ARNTL expression at the 4-cell stage in human and an increase in expression of Clock and Per1 from the zygote to 2-cell stage in the mouse. Analysis of intronic reads (indicative of embryonic transcription) for bovine embryos indicated an absence of embryonic transcription. Immunoreactive CRY1 was not detected in the bovine blastocyst. Results indicate that the preimplantation mammalian embryo lacks a functional intrinsic clock although specific components of the clock mechanism could conceivably play a role in other functions in the embryo.
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Affiliation(s)
- Daniel L Stanton
- D Stanton, Animal Sciences, University of Florida, Gainesville, United States
| | - Alexander Graf
- A Graf, Laboratory for Functional Genome Analysis, Ludwig-Maximilians-Universität München, Munchen, Germany
| | - Tatiane Silva Maia
- T Maia, Animal Sciences, University of Florida, Gainesville, United States
| | - Helmut Blum
- H Blum, Laboratory of Functional Genomics, Ludwig-Maximilians-Universität München, Munchen, Germany
| | - Zongliang Carl Jiang
- Z Jiang, Animal Sciences, University of Florida, Gainesville, 32611-7011, United States
| | - Peter J Hansen
- P Hansen, Dept. of Animal Sciences, University of Florida, Gainesville, 32611-0910, United States
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20
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Nchioua R, Schundner A, Klute S, Koepke L, Hirschenberger M, Noettger S, Fois G, Zech F, Graf A, Krebs S, Braubach P, Blum H, Stenger S, Kmiec D, Frick M, Kirchhoff F, Sparrer KM. Reduced replication but increased interferon resistance of SARS-CoV-2 Omicron BA.1. Life Sci Alliance 2023; 6:e202201745. [PMID: 36977594 PMCID: PMC10053418 DOI: 10.26508/lsa.202201745] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 09/29/2022] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 03/29/2023] Open
Abstract
The IFN system constitutes a powerful antiviral defense machinery. Consequently, effective IFN responses protect against severe COVID-19 and exogenous IFNs inhibit SARS-CoV-2 in vitro. However, emerging SARS-CoV-2 variants of concern (VOCs) may have evolved reduced IFN sensitivity. Here, we determined differences in replication and IFN susceptibility of an early SARS-CoV-2 isolate (NL-02-2020) and the Alpha, Beta, Gamma, Delta, and Omicron VOCs in Calu-3 cells, iPSC-derived alveolar type-II cells (iAT2) and air-liquid interface (ALI) cultures of primary human airway epithelial cells. Our data show that Alpha, Beta, and Gamma replicated to similar levels as NL-02-2020. In comparison, Delta consistently yielded higher viral RNA levels, whereas Omicron was attenuated. All viruses were inhibited by type-I, -II, and -III IFNs, albeit to varying extend. Overall, Alpha was slightly less sensitive to IFNs than NL-02-2020, whereas Beta, Gamma, and Delta remained fully sensitive. Strikingly, Omicron BA.1 was least restricted by exogenous IFNs in all cell models. Our results suggest that enhanced innate immune evasion rather than higher replication capacity contributed to the effective spread of Omicron BA.1.
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Affiliation(s)
- Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Annika Schundner
- Institute of General Physiology, Ulm University Medical Center, Ulm, Germany
| | - Susanne Klute
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Lennart Koepke
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | | | - Sabrina Noettger
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Giorgio Fois
- Institute of General Physiology, Ulm University Medical Center, Ulm, Germany
| | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Peter Braubach
- Hannover Medical School, Institute for Pathology, Hannover, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Steffen Stenger
- Institute for Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
| | - Dorota Kmiec
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Manfred Frick
- Institute of General Physiology, Ulm University Medical Center, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
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21
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Dichtl S, Diem G, Jäger M, Zaderer V, Lupoli G, Dächert C, Muenchhoff M, Graf A, Blum H, Keppler OT, Lass-Flörl C, Weiss G, Wilflingseder D, Posch W. Antiviral drugs block replication of highly immune-evasive Omicron subvariants ex vivo, but fail to reduce tissue inflammation. Antiviral Res 2023; 213:105581. [PMID: 36965526 PMCID: PMC10033493 DOI: 10.1016/j.antiviral.2023.105581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/20/2023] [Accepted: 03/15/2023] [Indexed: 03/25/2023]
Abstract
The identification of the SARS-CoV-2 Omicron variants BA.4/BA.5, BF.7 and BQ.1.1 immediately raised concerns regarding the efficacy of currently used monoclonal antibody therapies. Here we examined the activity of monoclonal antibody therapies and antiviral drugs against clinical specimens for SARS-CoV-2 Omicron BA.4/BA.5, BF.7 and BQ.1.1 employing an immunofluorescence neutralization assay. Further we explored treatment of BA.4/BA.5 infections with efficient antiviral drugs and monoclonal antibodies in a 3D model of primary human bronchial epithelial cells. We found that the antiviral drugs Molnupiravir, Nirmatrelvir and Remdesivir efficiently inhibit BA.4/BA.5, BF.7 and BQ.1.1 replication. In contrast, only the monoclonal antibody Cilgavimab exerted an inhibitory effect, while Tixagevimab, Regdanvimab and Sotrovimab lost their efficacy against BA.4/BA.5. We found that only the prophylactic treatment with Cilgavimab impacted on tissue inflammation by reducing intracellular complement component 3 (C3) activation following BA.4/BA.5 infection in primary human airway epithelial grown in air-liquid-interphase, which was not the case when using antiviral drugs or Cilgavimab after establishment of infection. Of note, all tested monoclonal antibodies had no neutralizing activity during infection by BF.7 and BQ.1.1 variants. Our results suggest that despite a marked reduction of viral replication, potent antiviral drugs fail to reduce tissue levels of inflammatory compounds such as C3, which can still result in tissue destruction.
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Affiliation(s)
- Stefanie Dichtl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gabriel Diem
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Michael Jäger
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Viktoria Zaderer
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gaia Lupoli
- Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Christopher Dächert
- Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Günter Weiss
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Doris Wilflingseder
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria.
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria.
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22
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Kufner CL, Krebs S, Fischaleck M, Philippou-Massier J, Blum H, Bucher DB, Braun D, Zinth W, Mast CB. Sequence dependent UV damage of complete pools of oligonucleotides. Sci Rep 2023; 13:2638. [PMID: 36788271 PMCID: PMC9929323 DOI: 10.1038/s41598-023-29833-0] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Understanding the sequence-dependent DNA damage formation requires probing a complete pool of sequences over a wide dose range of the damage-causing exposure. We used high throughput sequencing to simultaneously obtain the dose dependence and quantum yields for oligonucleotide damages for all possible 4096 DNA sequences with hexamer length. We exposed the DNA to ultraviolet radiation at 266 nm and doses of up to 500 absorbed photons per base. At the dimer level, our results confirm existing literature values of photodamage, whereas we now quantified the susceptibility of sequence motifs to UV irradiation up to previously inaccessible polymer lengths. This revealed the protective effect of the sequence context in preventing the formation of UV-lesions. For example, the rate to form dipyrimidine lesions is strongly reduced by nearby guanine bases. Our results provide a complete picture of the sensitivity of oligonucleotides to UV irradiation and allow us to predict their abundance in high-UV environments.
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Affiliation(s)
- Corinna L. Kufner
- grid.38142.3c000000041936754XHarvard-Smithsonian Center for Astrophysics, Department of Astronomy, Harvard University, 60 Garden Street, Cambridge, MA 02138 USA
| | - Stefan Krebs
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Marlis Fischaleck
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Julia Philippou-Massier
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Helmut Blum
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Dominik B. Bucher
- grid.6936.a0000000123222966Chemistry Department, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Dieter Braun
- grid.5252.00000 0004 1936 973XSystems Biophysics, Ludwig Maximilians University Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Wolfgang Zinth
- grid.5252.00000 0004 1936 973XBiomolecular Optics and Center for Integrated Protein Science, Ludwig Maximilians University Munich, Oettingenstrasse 67, 80538 Munich, Germany
| | - Christof B. Mast
- grid.5252.00000 0004 1936 973XSystems Biophysics, Ludwig Maximilians University Munich, Amalienstr. 54, 80799 Munich, Germany
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23
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Osterman A, Badell I, Dächert C, Schneider N, Kaufmann AY, Öztan GN, Huber M, Späth PM, Stern M, Autenrieth H, Muenchhoff M, Graf A, Krebs S, Blum H, Czibere L, Durner J, Kaderali L, Baldauf HM, Keppler OT. Variable detection of Omicron-BA.1 and -BA.2 by SARS-CoV-2 rapid antigen tests. Med Microbiol Immunol 2023; 212:13-23. [PMID: 36370197 PMCID: PMC9660148 DOI: 10.1007/s00430-022-00752-7] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/22/2022] [Indexed: 11/15/2022]
Abstract
During 2022, the COVID-19 pandemic has been dominated by the variant of concern (VoC) Omicron (B.1.1.529) and its rapidly emerging subvariants, including Omicron-BA.1 and -BA.2. Rapid antigen tests (RATs) are part of national testing strategies to identify SARS-CoV-2 infections on site in a community setting or to support layman's diagnostics at home. We and others have recently demonstrated an impaired RAT detection of infections caused by Omicron-BA.1 compared to Delta. Here, we evaluated the performance of five SARS-CoV-2 RATs in a single-centre laboratory study examining a total of 140 SARS-CoV-2 PCR-positive respiratory swab samples, 70 Omicron-BA.1 and 70 Omicron-BA.2, as well as 52 SARS-CoV-2 PCR-negative swabs collected from March 8th until April 10th, 2022. One test did not meet minimal criteria for specificity. In an assessment of the analytical sensitivity in clinical specimen, the 50% limit of detection (LoD50) ranged from 4.2 × 104 to 9.2 × 105 RNA copies subjected to the RAT for Omicron-BA.1 compared to 1.3 × 105 to 1.5 × 106 for Omicron-BA.2. Overall, intra-assay differences for the detection of Omicron-BA.1-containing and Omicron-BA.2-containing samples were non-significant, while a marked overall heterogeneity among the five RATs was observed. To score positive in these point-of-care tests, up to 22-fold (LoD50) or 68-fold (LoD95) higher viral loads were required for the worst performing compared to the best performing RAT. The rates of true-positive test results for these Omicron subvariant-containing samples in the highest viral load category (Ct values < 25) ranged between 44.7 and 91.1%, while they dropped to 8.7 to 22.7% for samples with intermediate Ct values (25-30). In light of recent reports on the emergence of two novel Omicron-BA.2 subvariants, Omicron-BA.2.75 and BJ.1, awareness must be increased for the overall reduced detection rate and marked differences in RAT performance for these Omicron subvariants.
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Affiliation(s)
- Andreas Osterman
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Irina Badell
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Christopher Dächert
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Nikolas Schneider
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Anna-Yasemin Kaufmann
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Gamze Naz Öztan
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Melanie Huber
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia M Späth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Marcel Stern
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Hanna Autenrieth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | | | - Jürgen Durner
- Labor Becker MVZ GbR, Munich, Germany
- Department of Conservative Dentistry and Periodontology, University Hospital, LMU München, Munich, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Hanna-Mari Baldauf
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
| | - Oliver T Keppler
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany.
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24
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Molitor L, Klostermann M, Bacher S, Merl-Pham J, Spranger N, Burczyk S, Ketteler C, Rusha E, Tews D, Pertek A, Proske M, Busch A, Reschke S, Feederle R, Hauck S, Blum H, Drukker M, Fischer-Posovszky P, König J, Zarnack K, Niessing D. Depletion of the RNA-binding protein PURA triggers changes in posttranscriptional gene regulation and loss of P-bodies. Nucleic Acids Res 2023; 51:1297-1316. [PMID: 36651277 PMCID: PMC9943675 DOI: 10.1093/nar/gkac1237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 01/19/2023] Open
Abstract
The RNA-binding protein PURA has been implicated in the rare, monogenetic, neurodevelopmental disorder PURA Syndrome. PURA binds both DNA and RNA and has been associated with various cellular functions. Only little is known about its main cellular roles and the molecular pathways affected upon PURA depletion. Here, we show that PURA is predominantly located in the cytoplasm, where it binds to thousands of mRNAs. Many of these transcripts change abundance in response to PURA depletion. The encoded proteins suggest a role for PURA in immune responses, mitochondrial function, autophagy and processing (P)-body activity. Intriguingly, reduced PURA levels decrease the expression of the integral P-body components LSM14A and DDX6 and strongly affect P-body formation in human cells. Furthermore, PURA knockdown results in stabilization of P-body-enriched transcripts, whereas other mRNAs are not affected. Hence, reduced PURA levels, as reported in patients with PURA Syndrome, influence the formation and composition of this phase-separated RNA processing machinery. Our study proposes PURA Syndrome as a new model to study the tight connection between P-body-associated RNA regulation and neurodevelopmental disorders.
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Affiliation(s)
| | | | - Sabrina Bacher
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Juliane Merl-Pham
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Nadine Spranger
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Sandra Burczyk
- Institute of Pharmaceutical Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Carolin Ketteler
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Ejona Rusha
- Induced Pluripotent Stem Cell Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Daniel Tews
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, 89070 Ulm, Germany
| | - Anna Pertek
- Induced Pluripotent Stem Cell Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Marcel Proske
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany,Institute of Pharmaceutical Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Sarah Reschke
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Regina Feederle
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Stefanie M Hauck
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Micha Drukker
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany,Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, 2333 CC Leiden, The Netherlands
| | - Pamela Fischer-Posovszky
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, 89070 Ulm, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Kathi Zarnack
- Correspondence may also be addressed to Kathi Zarnack. Tel: +49 69 798 42506; Fax: +49 69 798 763 42506;
| | - Dierk Niessing
- To whom correspondence should be addressed. Tel: +49 731 50 23160; Fax: +49 731 50 23169;
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25
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Hoppe JM, Füeßl LU, Hartmann K, Hofmann-Lehmann R, Graf A, Krebs S, Blum H, Badell I, Keppler OT, Muenchhoff M. Secondary zoonotic dog-to-human transmission of SARS-CoV-2 suggested by timeline but refuted by viral genome sequencing. Infection 2023; 51:253-259. [PMID: 35986880 PMCID: PMC9392066 DOI: 10.1007/s15010-022-01902-y] [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: 04/14/2022] [Accepted: 07/28/2022] [Indexed: 01/31/2023]
Abstract
PURPOSE The risk of secondary zoonotic transmission of SARS-CoV-2 from pet animals remains unclear. Here, we report on a 44 year old Caucasian male presenting to our clinic with COVID-19 pneumonia, who reported that his dog displayed respiratory signs shortly prior to his infection. The dog tested real-time-PCR (RT-PCR) positive for SARS-CoV-2 RNA and the timeline of events suggested a transmission from the dog to the patient. METHODS RT-PCR and serological assays were used to confirm SARS-CoV-2 infection in the nasopharyngeal tract in the dog and the patient. We performed SARS-CoV-2-targeted amplicon-based next generation sequencing of respiratory samples from the dog and patient for sequence comparisons. RESULTS SARS-CoV-2 infection of the dog was confirmed by three independent PCR-positive pharyngeal swabs and subsequent seroconversion. Sequence analysis identified two separate SARS-CoV-2 lineages in the canine and the patient's respiratory samples. The timeline strongly suggested dog-to-human transmission, yet due to the genetic distance of the canine and the patient's samples paired-transmission was highly unlikely. CONCLUSION The results of this case support current knowledge about the low risk of secondary zoonotic dog-to-human transmissions of SARS-CoV-2 and emphasizes the strength of genomic sequencing in deciphering viral transmission chains.
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Affiliation(s)
- John M. Hoppe
- grid.411095.80000 0004 0477 2585Medizinische Klinik und Poliklinik IV, Division of Nephrology, LMU Klinikum, Munich, Germany
| | - Louise U. Füeßl
- grid.411095.80000 0004 0477 2585Medizinische Klinik und Poliklinik IV, Division of Nephrology, LMU Klinikum, Munich, Germany
| | - Katrin Hartmann
- grid.5252.00000 0004 1936 973XMedizinische Kleintierklinik, Zentrum für Klinische Tiermedizin, LMU München, Munich, Germany
| | - Regina Hofmann-Lehmann
- grid.7400.30000 0004 1937 0650Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Alexander Graf
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Irina Badell
- grid.5252.00000 0004 1936 973XMax von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Oliver T. Keppler
- grid.5252.00000 0004 1936 973XMax von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany ,grid.452463.2German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Maximilian Muenchhoff
- grid.5252.00000 0004 1936 973XMax von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany ,grid.452463.2German Center for Infection Research (DZIF), Partner Site, Munich, Germany
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26
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Rabaglino MB, Forde N, Besenfelder U, Havlicek V, Blum H, Graf A, Wolf E, Lonergan P. 90 Influence of the maternal environment during the period of embryonic genome activation on the Day-4 embryo transcriptome. Reprod Fertil Dev 2022. [DOI: 10.1071/rdv35n2ab90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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27
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Deschler K, Rademacher J, Lacher SM, Huth A, Utzt M, Krebs S, Blum H, Haibel H, Proft F, Protopopov M, Rodriguez VR, Beltrán E, Poddubnyy D, Dornmair K. Antigen-specific immune reactions by expanded CD8 + T cell clones from HLA-B*27-positive patients with spondyloarthritis. J Autoimmun 2022; 133:102901. [PMID: 36115212 DOI: 10.1016/j.jaut.2022.102901] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 12/13/2022]
Abstract
Spondyloarthritis (SpA) is a chronic inflammatory disease that is tightly linked to HLA-B*27 but the pathophysiological basis of this link is still unknown. It is discussed whether either the instability of HLA-B*27 molecules triggers predominantly innate immune reactions or yet unknown antigenic peptides presented by HLA-B*27 induce adaptive autoimmune reactions by CD8+ T cells. To analyze the pathogenesis of SpA, we here investigated the T cell receptor (TCR) usage and whole transcriptomes of CD8+ single cells from synovial fluid of HLA-B*27-positive SpA patients and HLA-B*27-negative controls. In HLA-B*27-positive patients, we confirmed preferential expression of several TCR β-chain families, found even more restricted usage of particular TCR α-chains, assigned matching TCR αβ-chain pairs with homologous CDR3-sequences, and detected identical TCR-chains in different patients. Gene expression analyses by single cell mRNAseq revealed that genes specific for the tissue resident memory phenotype, exhaustion, and apoptosis were particularly highly expressed in expanded clonotypes from HLA-B*27-positive SpA patients. Together, several independent lines of evidence argue in favor of an (auto)antigenic peptide related pathogenesis.
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Affiliation(s)
- Katharina Deschler
- Institute of Clinical Neuroimmunology, University Hospital, LMU Munich, Munich, Germany; Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Judith Rademacher
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Gastroenterology, Infectiology and Rheumatologie (including Nutrition Medicine), Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Germany
| | - Sonja M Lacher
- Institute of Clinical Neuroimmunology, University Hospital, LMU Munich, Munich, Germany; Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Alina Huth
- Institute of Clinical Neuroimmunology, University Hospital, LMU Munich, Munich, Germany; Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Markus Utzt
- Institute of Clinical Neuroimmunology, University Hospital, LMU Munich, Munich, Germany; Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center of the LMU Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center of the LMU Munich, Germany
| | - Hildrun Haibel
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Gastroenterology, Infectiology and Rheumatologie (including Nutrition Medicine), Germany
| | - Fabian Proft
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Gastroenterology, Infectiology and Rheumatologie (including Nutrition Medicine), Germany
| | - Mikhail Protopopov
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Gastroenterology, Infectiology and Rheumatologie (including Nutrition Medicine), Germany
| | - Valeria Rios Rodriguez
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Gastroenterology, Infectiology and Rheumatologie (including Nutrition Medicine), Germany
| | - Eduardo Beltrán
- Institute of Clinical Neuroimmunology, University Hospital, LMU Munich, Munich, Germany; Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Denis Poddubnyy
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Gastroenterology, Infectiology and Rheumatologie (including Nutrition Medicine), Germany; Epidemiology unit, German Rheumatism Research Centre, Berlin, Germany.
| | - Klaus Dornmair
- Institute of Clinical Neuroimmunology, University Hospital, LMU Munich, Munich, Germany; Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany.
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28
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Khatamzas E, Antwerpen MH, Rehn A, Graf A, Hellmuth JC, Hollaus A, Mohr AW, Gaitzsch E, Weiglein T, Georgi E, Scherer C, Stecher SS, Gruetzner S, Blum H, Krebs S, Reischer A, Leutbecher A, Subklewe M, Dick A, Zange S, Girl P, Müller K, Weigert O, Hopfner KP, Stemmler HJ, von Bergwelt-Baildon M, Keppler OT, Wölfel R, Muenchhoff M, Moosmann A. Accumulation of mutations in antibody and CD8 T cell epitopes in a B cell depleted lymphoma patient with chronic SARS-CoV-2 infection. Nat Commun 2022; 13:5586. [PMID: 36151076 PMCID: PMC9508331 DOI: 10.1038/s41467-022-32772-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 08/15/2022] [Indexed: 11/29/2022] Open
Abstract
Antibodies against the spike protein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) can drive adaptive evolution in immunocompromised patients with chronic infection. Here we longitudinally analyze SARS-CoV-2 sequences in a B cell-depleted, lymphoma patient with chronic, ultimately fatal infection, and identify three mutations in the spike protein that dampen convalescent plasma-mediated neutralization of SARS-CoV-2. Additionally, four mutations emerge in non-spike regions encoding three CD8 T cell epitopes, including one nucleoprotein epitope affected by two mutations. Recognition of each mutant peptide by CD8 T cells from convalescent donors is reduced compared to its ancestral peptide, with additive effects resulting from double mutations. Querying public SARS-CoV-2 sequences shows that these mutations have independently emerged as homoplasies in circulating lineages. Our data thus suggest that potential impacts of CD8 T cells on SARS-CoV-2 mutations, at least in those with humoral immunodeficiency, warrant further investigation to inform on vaccine design. SARS-CoV-2 mutations associated with the escape from antibody-mediated neutralization have been widely reported. Here, in a patient with defective antibody responses, the authors find a potential association between SARS-CoV-2 mutations and CD8 T alterations to implicate possible contributions of CD8 T cells in evasion of SARS-CoV-2 from host immunity.
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Affiliation(s)
- Elham Khatamzas
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany. .,Division of Infectious Diseases and Tropical Medicine, Center for Infectious Diseases, Heidelberg Hospital, Heidelberg, Germany. .,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.
| | - Markus H Antwerpen
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Alexandra Rehn
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians University Munich, Munich, Germany
| | - Johannes Christian Hellmuth
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Alexandra Hollaus
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Anne-Wiebe Mohr
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Erik Gaitzsch
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Tobias Weiglein
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Enrico Georgi
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Clemens Scherer
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,Department of Medicine I, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Stephanie-Susanne Stecher
- Department of Medicine II, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Stefanie Gruetzner
- Institute for Transfusion Medicine and Haemostasis, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians University Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians University Munich, Munich, Germany
| | - Anna Reischer
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Alexandra Leutbecher
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Marion Subklewe
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Andrea Dick
- Laboratory for Immunogenetics, University of Munich, LMU, Munich, Germany
| | - Sabine Zange
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Philipp Girl
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Katharina Müller
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Oliver Weigert
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hans-Joachim Stemmler
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Michael von Bergwelt-Baildon
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Oliver T Keppler
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.,Max von Pettenkofer Institute & Gene Center, Virology, Faculty of Medicine, Ludwig-Maximilians University, Munich, Germany
| | - Roman Wölfel
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Maximilian Muenchhoff
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.,Max von Pettenkofer Institute & Gene Center, Virology, Faculty of Medicine, Ludwig-Maximilians University, Munich, Germany
| | - Andreas Moosmann
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
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29
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Lagler DK, Hannemann E, Eck K, Klawatsch J, Seichter D, Russ I, Mendel C, Lühken G, Krebs S, Blum H, Upadhyay M, Medugorac I. Fine-mapping and identification of candidate causal genes for tail length in the Merinolandschaf breed. Commun Biol 2022; 5:918. [PMID: 36068271 PMCID: PMC9448734 DOI: 10.1038/s42003-022-03854-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 04/04/2022] [Accepted: 08/16/2022] [Indexed: 12/14/2022] Open
Abstract
Docking the tails of lambs in long-tailed sheep breeds is a common practice worldwide. But this practice is associated with pain. Breeding for a shorter tail could offer an alternative. Therefore, this study aimed to analyze the natural tail length variation in the Merinolandschaf and to identify causal alleles for the short tail phenotype segregating within long-tailed breeds. We used SNP-based association analysis and haplotype-based mapping in 362 genotyped (Illumina OvineSNP50) and phenotyped Merinolandschaf lambs. Genome-wide significant regions were capture sequenced in 48 lambs and comparatively analyzed in various long and short-tailed sheep breeds and wild sheep subspecies. Here we show a SNP located in the first exon of HOXB13 and a SINE element located in the promotor of HOXB13 as promising candidates. These results enable more precise breeding towards shorter tails, improve animal welfare by amplification of ancestral alleles and contribute to a better understanding of differential embryonic development. Using SNP-association analysis and genetic mapping, a SNP and an insertion in and close to HOXB13 associated with short tail length is identified in Merino sheep, which may be a target for safely selecting shorter tails and improving sheep welfare.
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Affiliation(s)
- Dominik Karl Lagler
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany.,Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Elisabeth Hannemann
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany
| | - Kim Eck
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany.,Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Jürgen Klawatsch
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany.,Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Doris Seichter
- Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Ingolf Russ
- Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Christian Mendel
- Institute for Animal Breeding, Bavarian State Research Center for Agriculture, Prof.-Dürrwaechter-Platz 1, 85586, Poing, Germany
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, JLU Gießen, Ludwigstr. 21, 35390, Gießen, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-University Munich, 80539, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-University Munich, 80539, Munich, Germany
| | - Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany.
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30
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Kuhn LB, Valentin S, Stojanovic K, Strobl DC, Babushku T, Wang Y, Rambold U, Scheffler L, Grath S, John-Robbert D, Blum H, Feuchtinger A, Blutke A, Weih F, Kitamura D, Rad R, Strobl LJ, Zimber-Strobl U. RelB contributes to the survival, migration and lymphomagenesis of B cells with constitutively active CD40 signaling. Front Immunol 2022; 13:913275. [PMID: 36110848 PMCID: PMC9468873 DOI: 10.3389/fimmu.2022.913275] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/04/2022] [Indexed: 11/14/2022] Open
Abstract
Activation of CD40-signaling contributes to the initiation, progression and drug resistance of B cell lymphomas. We contributed to this knowledge by showing that constitutive CD40-signaling in B cells induces B cell hyperplasia and finally B cell lymphoma development in transgenic mice. CD40 activates, among others, the non-canonical NF-ĸB signaling, which is constitutively activated in several human B cell lymphomas and is therefore presumed to contribute to lymphopathogenesis. This prompted us to study the regulatory role of the non-canonical NF-ĸB transcription factor RelB in lymphomagenesis. To this end, we crossed mice expressing a constitutively active CD40 receptor in B cells with conditional RelB-KO mice. Ablation of RelB attenuated pre-malignant B cell expansion, and resulted in an impaired survival and activation of long-term CD40-stimulated B cells. Furthermore, we found that hyperactivation of non-canonical NF-кB signaling enhances the retention of B cells in the follicles of secondary lymphoid organs. RNA-Seq-analysis revealed that several genes involved in B-cell migration, survival, proliferation and cytokine signaling govern the transcriptional differences modulated by the ablation of RelB in long-term CD40-stimulated B cells. Inactivation of RelB did not abrogate lymphoma development. However, lymphomas occurred with a lower incidence and had a longer latency period. In summary, our data suggest that RelB, although it is not strictly required for malignant transformation, accelerates the lymphomagenesis of long-term CD40-stimulated B cells by regulating genes involved in migration, survival and cytokine signaling.
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Affiliation(s)
- Laura B. Kuhn
- Institute of Lung Health and Immunity, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Stefanie Valentin
- Institute of Lung Health and Immunity, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Kristina Stojanovic
- Institute of Lung Health and Immunity, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Daniel C. Strobl
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Tea Babushku
- Institute of Lung Health and Immunity, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Molecular Oncology and Functional Genomics, Technical University of Munich (TUM) School of Medicine, Technical University of Munich, Munich, Germany
| | - Yan Wang
- Institute of Lung Health and Immunity, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ursula Rambold
- Institute of Asthma and Allergy Prevention, Helmholtz Zentrum München, German Research Center for Environmental Health., Munich, Germany
| | - Laura Scheffler
- Institute of Lung Health and Immunity, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Sonja Grath
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität (LMU), Planegg-Martinsried, Germany
| | - Dorothy John-Robbert
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität (LMU), Planegg-Martinsried, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene-Center, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Andreas Blutke
- Research Unit Analytical Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Falk Weih
- Research Group Immunology, Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Daisuke Kitamura
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Japan
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, Technical University of Munich (TUM) School of Medicine, Technical University of Munich, Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Cancer Consortium (DKTK), Heidelberg, Germany
| | - Lothar J. Strobl
- Institute of Lung Health and Immunity, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ursula Zimber-Strobl
- Institute of Lung Health and Immunity, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- *Correspondence: Ursula Zimber-Strobl,
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31
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Bergant V, Yamada S, Grass V, Tsukamoto Y, Lavacca T, Krey K, Mühlhofer MT, Wittmann S, Ensser A, Herrmann A, Vom Hemdt A, Tomita Y, Matsuyama S, Hirokawa T, Huang Y, Piras A, Jakwerth CA, Oelsner M, Thieme S, Graf A, Krebs S, Blum H, Kümmerer BM, Stukalov A, Schmidt-Weber CB, Igarashi M, Gramberg T, Pichlmair A, Kato H. Attenuation of SARS-CoV-2 replication and associated inflammation by concomitant targeting of viral and host cap 2'-O-ribose methyltransferases. EMBO J 2022; 41:e111608. [PMID: 35833542 PMCID: PMC9350232 DOI: 10.15252/embj.2022111608] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 05/08/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 12/12/2022] Open
Abstract
The SARS‐CoV‐2 infection cycle is a multistage process that relies on functional interactions between the host and the pathogen. Here, we repurposed antiviral drugs against both viral and host enzymes to pharmaceutically block methylation of the viral RNA 2'‐O‐ribose cap needed for viral immune escape. We find that the host cap 2'‐O‐ribose methyltransferase MTr1 can compensate for loss of viral NSP16 methyltransferase in facilitating virus replication. Concomitant inhibition of MTr1 and NSP16 efficiently suppresses SARS‐CoV‐2 replication. Using in silico target‐based drug screening, we identify a bispecific MTr1/NSP16 inhibitor with anti‐SARS‐CoV‐2 activity in vitro and in vivo but with unfavorable side effects. We further show antiviral activity of inhibitors that target independent stages of the host SAM cycle providing the methyltransferase co‐substrate. In particular, the adenosylhomocysteinase (AHCY) inhibitor DZNep is antiviral in in vitro, in ex vivo, and in a mouse infection model and synergizes with existing COVID‐19 treatments. Moreover, DZNep exhibits a strong immunomodulatory effect curbing infection‐induced hyperinflammation and reduces lung fibrosis markers ex vivo. Thus, multispecific and metabolic MTase inhibitors constitute yet unexplored treatment options against COVID‐19.
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Affiliation(s)
- Valter Bergant
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Shintaro Yamada
- Institute of Cardiovascular Immunology, University Hospital Bonn (UKB), Bonn, Germany
| | - Vincent Grass
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Yuta Tsukamoto
- Institute of Cardiovascular Immunology, University Hospital Bonn (UKB), Bonn, Germany
| | - Teresa Lavacca
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Karsten Krey
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Maria-Teresa Mühlhofer
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Sabine Wittmann
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Armin Ensser
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Alexandra Herrmann
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Anja Vom Hemdt
- Institute of Virology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Yuriko Tomita
- Department of Virology III, National Institute of Infectious Diseases (NIID), Tokyo, Japan
| | - Shutoku Matsuyama
- Department of Virology III, National Institute of Infectious Diseases (NIID), Tokyo, Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan.,Division of Biomedical Science, University of Tsukuba, Tsukuba, Japan.,Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Yiqi Huang
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Antonio Piras
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Constanze A Jakwerth
- Center for Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Center Munich, German Research Center for Environmental Health, Member of the German Center for Lung Research (DZL), CPC-M, Munich, Germany
| | - Madlen Oelsner
- Center for Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Center Munich, German Research Center for Environmental Health, Member of the German Center for Lung Research (DZL), CPC-M, Munich, Germany
| | - Susanne Thieme
- Laboratory for functional genome analysis (LAFUGA), Gene Centre, Ludwig Maximilian University of Munich (LMU), Munich, Germany
| | - Alexander Graf
- Laboratory for functional genome analysis (LAFUGA), Gene Centre, Ludwig Maximilian University of Munich (LMU), Munich, Germany
| | - Stefan Krebs
- Laboratory for functional genome analysis (LAFUGA), Gene Centre, Ludwig Maximilian University of Munich (LMU), Munich, Germany
| | - Helmut Blum
- Laboratory for functional genome analysis (LAFUGA), Gene Centre, Ludwig Maximilian University of Munich (LMU), Munich, Germany
| | - Beate M Kümmerer
- Institute of Virology, Medical Faculty, University of Bonn, Bonn, Germany.,German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Bonn, Germany
| | - Alexey Stukalov
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Carsten B Schmidt-Weber
- Center for Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Center Munich, German Research Center for Environmental Health, Member of the German Center for Lung Research (DZL), CPC-M, Munich, Germany
| | - Manabu Igarashi
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan.,Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Thomas Gramberg
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Andreas Pichlmair
- Institute of Virology, School of Medicine, Technical University of Munich (TUM), Munich, Germany.,German Center for Infection Research (DZIF), Munich partner site, Germany
| | - Hiroki Kato
- Institute of Cardiovascular Immunology, University Hospital Bonn (UKB), Bonn, Germany
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Nchioua R, Schundner A, Kmiec D, Prelli Bozzo C, Zech F, Koepke L, Graf A, Krebs S, Blum H, Frick M, Sparrer KMJ, Kirchhoff F. SARS-CoV-2 Variants of Concern Hijack IFITM2 for Efficient Replication in Human Lung Cells. J Virol 2022; 96:e0059422. [PMID: 35543509 PMCID: PMC9175628 DOI: 10.1128/jvi.00594-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 12/17/2022] Open
Abstract
It has recently been shown that an early SARS-CoV-2 isolate (NL-02-2020) hijacks interferon-induced transmembrane proteins (IFITMs) for efficient replication in human lung cells, cardiomyocytes, and gut organoids. To date, several "variants of concern" (VOCs) showing increased infectivity and resistance to neutralization have emerged and globally replaced the early viral strains. Here, we determined whether the five current SARS-CoV-2 VOCs (Alpha, Beta, Gamma, Delta, and Omicron) maintained the dependency on IFITM proteins for efficient replication. We found that depletion of IFITM2 strongly reduces viral RNA production by all VOCs in the human epithelial lung cancer cell line Calu-3. Silencing of IFITM1 had modest effects, while knockdown of IFITM3 resulted in an intermediate phenotype. Strikingly, depletion of IFITM2 generally reduced infectious virus production by more than 4 orders of magnitude. In addition, an antibody directed against the N terminus of IFITM2 inhibited SARS-CoV-2 VOC replication in induced pluripotent stem cell (iPSC)-derived alveolar epithelial type II cells, thought to represent major viral target cells in the lung. In conclusion, endogenously expressed IFITM proteins (especially IFITM2) are critical cofactors for efficient replication of genuine SARS-CoV-2 VOCs, including the currently dominant Omicron variant. IMPORTANCE Recent data indicate that SARS-CoV-2 requires endogenously expressed IFITM proteins for efficient infection. However, the results were obtained with an early SARS-CoV-2 isolate. Thus, it remained to be determined whether IFITMs are also important cofactors for infection of emerging SARS-CoV-2 VOCs that outcompeted the original strains in the meantime. This includes the Omicron VOC, which currently dominates the pandemic. Here, we show that depletion of endogenous IFITM2 expression almost entirely prevents productive infection of Alpha, Beta, Gamma, Delta, and Omicron SARS-CoV-2 VOCs in human lung cells. In addition, an antibody targeting the N terminus of IFITM2 inhibited SARS-CoV-2 VOC replication in iPSC-derived alveolar epithelial type II cells. Our results show that SARS-CoV-2 VOCs, including the currently dominant Omicron variant, are strongly dependent on IFITM2 for efficient replication, suggesting a key proviral role of IFITMs in viral transmission and pathogenicity.
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Affiliation(s)
- Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Annika Schundner
- Institute of General Physiology, Ulm University Medical Center, Ulm, Germany
| | - Dorota Kmiec
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | | | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Lennart Koepke
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Manfred Frick
- Institute of General Physiology, Ulm University Medical Center, Ulm, Germany
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
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Rademacher J, Deschler K, Lacher S, Huth A, Utzt M, Krebs S, Blum H, Beltrán E, Poddubnyy D, Dornmair K. OP0104 EXPANDED CD8+ T CELL CLONES FROM HLA-B*27-POSITIVE PATIENTS WITH SPONDYLOARTHRITIS SHOW SIGNS OF ANTIGEN-EXPERIENCE. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.3271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BackgroundThe pathogenesis of Spondyloarthritis (SpA) remains unknown but its strong association with some alleles of HLA-B*27 is peculiar. The arthritogenic antigen hypothesis assumes the existence of specific peptides presented by risk-conferring HLA-B*27 alleles to antigen-specific CD8+ T cells, which then initiate or sustain autoimmune reactions. Several studies analyzing T cell receptor (TCR) repertoire found preferred Variable TCR chains and motifs in the hypervariable complementary determining region (CDR) 3, but analyzed only TCR β-chains in bulk analyses1,2.ObjectivesTo analyze full sequence information of TCR including matching α- and β-chains from single CD8+ T cells and characterize the transcriptomes of expanded and non-expanded clonotypes in synovial fluid (SF) of SpA patients.MethodsWe included 17 patients with active gonarthritis: 10 patients with HLA-B27 positive (B27pos) SpA, 4 with HLA-B27 negative (B27neg) SpA and 3 rheumatoid arthritis (RA) patients. Antigen-experienced CD8+ T cells were sorted out of SF by flow cytometry. Single cell sequencing was performed for all patients to analyze matching TCR α- and β-chains. For 7 patients (3 B27pos SpA, 2 B27neg SpA, 2 RA), additionally whole transcriptome analyses were performed.ResultsWe found strong biases when analyzing α and β chains of TCR Variable regions and CDR1 and CDR2 sequences (Figure 1 a,b): AV21, AV12-2, and AV17 were highly enriched in B27pos SpA as compared to B27neg subjects. Amongst the highest expressed clones, we could confirm enrichment for previously described TRBV genes as BV19, BV5-1 and BV6-2. We examined TCR α/β combinations and focused on those detected in at least three different B27pos SpA but not in any of the B27neg patients (Figure 1 c-f). The combinations TRBV19/TRAV21 and TRBV6-2/TRAV21 were most likely specific for B27pos SpA and might reflect interaction of these TCR chains with HLA-B*27. Sequences of CDR3 loops, which predominantly interact with HLA-bound antigenic peptides, revealed striking common structural motifs in α- and β-chains. Focusing on the most prominent TRAV21 chains pairing with TRBV19, 5-1 and 6-2 chains, revealed identical sequences in different patients and striking common structural motifs in α- and β-CDR3 sequences in other patients. Such marked similarities in the antigen-recognition loops of the β-chains associated with TRAV21 suggest common or highly similar antigens. Gene expression levels provided evidence that expanded cell populations had tissue resident memory (TRM) phenotypes (elevated expression of activation, migration and tissue retention markers, downregulated genes characteristic for T cell egress), while this phenotype was not very pronounced in non-expanded cells. Furthermore, markers for T cell exhaustion and apoptosis were elevated in expanded cells of B27pos SpA patients.Figure 1.Distinct TCRαβ V chain usage in expanded clones from HLA-B27 positive SpA patients. A,B Mean number of all productive TRAV (A) and TRBV (B) genes used in expanded, antigen-experienced CD8 T cell clones (>1% of all cells) from SF of 10 B27pos SpA, 4 B27neg SpA and 3 B27neg RA patients. C-F TRAV chains paired with TRBV19 (C), TRBV5-1 (D), TRBV6-2 (E), or TRBV chains paired with TRAV21 (F) with corresponding TRAJ spanning partners in expanded cells (frequency ≥2) from all 10 B27pos SpA. Number of chains are 1250 (C), 886 (D), 1220 (E), and 4006 (F).ConclusionAnalysis of single antigen experienced CD8+ T cells from SF of B27pos SpA patients revealed significant clonal expansions and common motifs in the CDR loops. Two of the four CDR1 and CDR2 loops were highly homologous suggesting that these loops interact with α-helices of HLA-B*27. Common motifs in CDR3 loops of expanded clonotypes suggest recognition of a limited set of antigenic peptides presented by HLA-B*27. Many of the expanded clonotypes showed a TRM phenotype, were exhausted and on the way to become apoptotic, which suggests that these clones had sustained contact to specific antigens.References[1]Komech, et al. Rheumatology 2018[2]Hanson, et al. A&R 2020AcknowledgementsWe thank all patients included in this study for their participation. This work was funded by the German Research Foundation (DFG) through grants DO 420/4 to KDo, PO 2124/2-1 to DP, and SyNergy (EXC 2145 SyNergy – ID 390857198) to KDo. Judith Rademacher and Katharina Deschler contributed equally. JR is participant in the BIH-Charité Clinician Scientist Program funded by the Charité –Universitätsmedizin Berlin and the Berlin Institute of Health. The authors would like to thank Martina Seipel for excellent technical assistance, Sabrina Sron for patient recruitment and study coordination, and Hildrun Haibel, Mikhail Protopopov, Fabian Proft, Valeria Rios Rodriguez and Laura Spiller for recruiting patients for this study.Disclosure of InterestsNone declared
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Osterman A, Badell I, Basara E, Stern M, Kriesel F, Eletreby M, Öztan GN, Huber M, Autenrieth H, Knabe R, Späth PM, Muenchhoff M, Graf A, Krebs S, Blum H, Durner J, Czibere L, Dächert C, Kaderali L, Baldauf HM, Keppler OT. Impaired detection of omicron by SARS-CoV-2 rapid antigen tests. Med Microbiol Immunol 2022; 211:105-117. [PMID: 35187580 PMCID: PMC8858605 DOI: 10.1007/s00430-022-00730-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [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: 02/09/2022] [Accepted: 02/12/2022] [Indexed: 01/25/2023]
Abstract
Since autumn 2020, rapid antigen tests (RATs) have been implemented in several countries as an important pillar of the national testing strategy to rapidly screen for infections on site during the SARS-CoV-2 pandemic. The current surge in infection rates around the globe is driven by the variant of concern (VoC) omicron (B.1.1.529). Here, we evaluated the performance of nine SARS-CoV-2 RATs in a single-centre laboratory study. We examined a total of 115 SARS-CoV-2 PCR-negative and 166 SARS-CoV-2 PCR-positive respiratory swab samples (101 omicron, 65 delta (B.1.617.2)) collected from October 2021 until January 2022 as well as cell culture-expanded clinical isolates of both VoCs. In an assessment of the analytical sensitivity in clinical specimen, the 50% limit of detection (LoD50) ranged from 1.77 × 106 to 7.03 × 107 RNA copies subjected to the RAT for omicron compared to 1.32 × 105 to 2.05 × 106 for delta. To score positive in these point-of-care tests, up to 10-fold (LoD50) or 101-fold (LoD95) higher virus loads were required for omicron- compared to delta-containing samples. The rates of true positive test results for omicron samples in the highest virus load category (Ct values < 25) ranged between 31.4 and 77.8%, while they dropped to 0-8.3% for samples with intermediate Ct values (25-30). Of note, testing of expanded virus stocks suggested a comparable RAT sensitivity of both VoCs, questioning the predictive value of this type of in vitro-studies for clinical performance. Given their importance for national test strategies in the current omicron wave, awareness must be increased for the reduced detection rate of omicron infections by RATs and a short list of suitable RATs that fulfill the minimal requirements of performance should be rapidly disclosed.
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Affiliation(s)
- Andreas Osterman
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Irina Badell
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Elif Basara
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Marcel Stern
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Fabian Kriesel
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Marwa Eletreby
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Gamze Naz Öztan
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Melanie Huber
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Hanna Autenrieth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Ricarda Knabe
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Patricia M Späth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Maximilian Muenchhoff
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Jürgen Durner
- Labor Becker MVZ GbR, Munich, Germany
- Department of Conservative Dentistry and Periodontology, University Hospital, LMU München, Goethestr. 70, 80336, Munich, Germany
| | | | - Christopher Dächert
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475, Greifswald, Germany.
| | - Hanna-Mari Baldauf
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany.
| | - Oliver T Keppler
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany.
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.
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Simmet K, Kurome M, Zakhartchenko V, Reichenbach HD, Springer C, Bähr A, Blum H, Philippou-Massier J, Wolf E. OCT4/POU5F1 is indispensable for the lineage differentiation of the inner cell mass in bovine embryos. FASEB J 2022; 36:e22337. [PMID: 35486003 DOI: 10.1096/fj.202101713rrr] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 04/10/2022] [Accepted: 04/21/2022] [Indexed: 01/01/2023]
Abstract
The mammalian blastocyst undergoes two lineage segregations, that is, formation of the trophectoderm and subsequently differentiation of the hypoblast (HB) from the inner cell mass, leaving the epiblast (EPI) as the remaining pluripotent lineage. To clarify the expression patterns of markers specific for these lineages in bovine embryos, we analyzed day 7, 9, and 12 blastocysts completely produced in vivo by staining for OCT4, NANOG, SOX2 (EPI), and GATA6, SOX17 (HB) and identified genes specific for these developmental stages in a global transcriptomics approach. To study the role of OCT4, we generated OCT4-deficient (OCT4 KO) embryos via somatic cell nuclear transfer or in vitro fertilization. OCT4 KO embryos reached the expanded blastocyst stage by day 8 but lost NANOG and SOX17 expression, while SOX2 and GATA6 were unaffected. Blastocysts transferred to recipient cows from day 6 to 9 expanded, but the OCT4 KO phenotype was not rescued by the uterine environment. Exposure of OCT4 KO embryos to exogenous FGF4 or chimeric complementation with OCT4 intact embryos did not restore NANOG or SOX17 in OCT4-deficient cells. Our data show that OCT4 is required cell autonomously for the maintenance of pluripotency of the EPI and differentiation of the HB in bovine embryos.
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Affiliation(s)
- Kilian Simmet
- Gene Center, Department of Veterinary Sciences, Institute of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models (CiMM), LMU Munich, Oberschleißheim, Germany
| | - Mayuko Kurome
- Gene Center, Department of Veterinary Sciences, Institute of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models (CiMM), LMU Munich, Oberschleißheim, Germany
| | - Valeri Zakhartchenko
- Gene Center, Department of Veterinary Sciences, Institute of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models (CiMM), LMU Munich, Oberschleißheim, Germany
| | | | - Claudia Springer
- Gene Center, Department of Veterinary Sciences, Institute of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models (CiMM), LMU Munich, Oberschleißheim, Germany
| | - Andrea Bähr
- Gene Center, Department of Veterinary Sciences, Institute of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models (CiMM), LMU Munich, Oberschleißheim, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Julia Philippou-Massier
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Eckhard Wolf
- Gene Center, Department of Veterinary Sciences, Institute of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models (CiMM), LMU Munich, Oberschleißheim, Germany.,Bavarian State Research Center for Agriculture, Institute of Animal Breeding, Poing, Germany
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36
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Stirm M, Fonteyne LM, Shashikadze B, Stöckl JB, Kurome M, Keßler B, Zakhartchenko V, Kemter E, Blum H, Arnold GJ, Matiasek K, Wanke R, Wurst W, Nagashima H, Knieling F, Walter MC, Kupatt C, Fröhlich T, Klymiuk N, Blutke A, Wolf E. Pig models for Duchenne muscular dystrophy – from disease mechanisms to validation of new diagnostic and therapeutic concepts. Neuromuscul Disord 2022; 32:543-556. [DOI: 10.1016/j.nmd.2022.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/22/2022] [Accepted: 04/22/2022] [Indexed: 12/13/2022]
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Dächert C, Muenchhoff M, Graf A, Autenrieth H, Bender S, Mairhofer H, Wratil PR, Thieme S, Krebs S, Grzimek-Koschewa N, Blum H, Keppler OT. Rapid and sensitive identification of omicron by variant-specific PCR and nanopore sequencing: paradigm for diagnostics of emerging SARS-CoV-2 variants. Med Microbiol Immunol 2022; 211:71-77. [PMID: 35061086 PMCID: PMC8780046 DOI: 10.1007/s00430-022-00728-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [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: 01/04/2022] [Accepted: 01/08/2022] [Indexed: 12/19/2022]
Abstract
On November 26, 2021, the World Health Organization classified B.1.1.529 as a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern (VoC), named omicron. Spike-gene dropouts in conventional SARS-CoV-2 PCR systems have been reported over the last weeks as indirect diagnostic evidence for the identification of omicron. Here, we report the combination of PCRs specific for heavily mutated sites in the spike gene and nanopore-based full-length genome sequencing for the rapid and sensitive identification of the first four COVID-19 patients diagnosed in Germany to be infected with omicron on November 28, 2021. This study will assist the unambiguous laboratory-based diagnosis and global surveillance for this highly contagious VoC with an unprecedented degree of humoral immune escape. Moreover, we propose that specialized diagnostic laboratories should continuously update their assays for variant-specific PCRs in the spike gene of SARS-CoV-2 to readily detect and diagnose emerging variants of interest and VoCs. The combination with established nanopore sequencing procedures allows both the rapid confirmation by whole genome sequencing as well as the sensitive identification of newly emerging variants of this pandemic β-coronavirus in years to come.
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Affiliation(s)
- Christopher Dächert
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Alexander Graf
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Hanna Autenrieth
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Sabine Bender
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Helga Mairhofer
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Paul R Wratil
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Susanne Thieme
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Natascha Grzimek-Koschewa
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany.
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Wratil PR, Stern M, Priller A, Willmann A, Almanzar G, Vogel E, Feuerherd M, Cheng CC, Yazici S, Christa C, Jeske S, Lupoli G, Vogt T, Albanese M, Mejías-Pérez E, Bauernfried S, Graf N, Mijocevic H, Vu M, Tinnefeld K, Wettengel J, Hoffmann D, Muenchhoff M, Daechert C, Mairhofer H, Krebs S, Fingerle V, Graf A, Steininger P, Blum H, Hornung V, Liebl B, Überla K, Prelog M, Knolle P, Keppler OT, Protzer U. Three exposures to the spike protein of SARS-CoV-2 by either infection or vaccination elicit superior neutralizing immunity to all variants of concern. Nat Med 2022; 28:496-503. [PMID: 35090165 DOI: 10.1038/s41591-022-01715-4] [Citation(s) in RCA: 154] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/25/2022] [Indexed: 11/09/2022]
Abstract
Infection-neutralizing antibody responses after SARS-CoV-2 infection or COVID-19 vaccination are an essential component of antiviral immunity. Antibody-mediated protection is challenged by the emergence of SARS-CoV-2 variants of concern (VoCs) with immune escape properties, such as omicron (B.1.1.529) that is rapidly spreading worldwide. Here, we report neutralizing antibody dynamics in a longitudinal cohort of COVID-19 convalescent and infection-naive individuals vaccinated with mRNA BNT162b2 by quantifying anti-SARS-CoV-2-spike antibodies and determining their avidity and neutralization capacity in serum. Using live-virus neutralization assays, we show that a superior infection-neutralizing capacity against all VoCs, including omicron, developed after either two vaccinations in convalescents or after a third vaccination or breakthrough infection of twice-vaccinated, naive individuals. These three consecutive spike antigen exposures resulted in an increasing neutralization capacity per anti-spike antibody unit and were paralleled by stepwise increases in antibody avidity. We conclude that an infection-plus-vaccination-induced hybrid immunity or a triple immunization can induce high-quality antibodies with superior neutralization capacity against VoCs, including omicron.
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Affiliation(s)
- Paul R Wratil
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.,German Centre for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Marcel Stern
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Alina Priller
- Institute of Molecular Immunology and Experimental Oncology, University Hospital rechts der Isar, Technical University of Munich (TUM), School of Medicine, Munich, Germany
| | - Annika Willmann
- Institute of Virology, Helmholtz Center Munich, Technical University of Munich (TUM), School of Medicine, Munich, Germany
| | - Giovanni Almanzar
- Pediatric Rheumatology / Special Immunology, Pediatrics Department, University Hospital Würzburg, Würzburg, Germany
| | - Emanuel Vogel
- Institute of Virology, Helmholtz Center Munich, Technical University of Munich (TUM), School of Medicine, Munich, Germany
| | - Martin Feuerherd
- Institute of Virology, Helmholtz Center Munich, Technical University of Munich (TUM), School of Medicine, Munich, Germany
| | - Cho-Chin Cheng
- Institute of Virology, Helmholtz Center Munich, Technical University of Munich (TUM), School of Medicine, Munich, Germany
| | - Sarah Yazici
- Institute of Molecular Immunology and Experimental Oncology, University Hospital rechts der Isar, Technical University of Munich (TUM), School of Medicine, Munich, Germany
| | - Catharina Christa
- Institute of Virology, Helmholtz Center Munich, Technical University of Munich (TUM), School of Medicine, Munich, Germany
| | - Samuel Jeske
- Institute of Virology, Helmholtz Center Munich, Technical University of Munich (TUM), School of Medicine, Munich, Germany
| | - Gaia Lupoli
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Tim Vogt
- Pediatric Rheumatology / Special Immunology, Pediatrics Department, University Hospital Würzburg, Würzburg, Germany
| | - Manuel Albanese
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.,National Institute of Molecular Genetics (INGM), Milano, Italy
| | - Ernesto Mejías-Pérez
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Stefan Bauernfried
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Natalia Graf
- Institute of Virology, Helmholtz Center Munich, Technical University of Munich (TUM), School of Medicine, Munich, Germany
| | - Hrvoje Mijocevic
- Institute of Virology, Helmholtz Center Munich, Technical University of Munich (TUM), School of Medicine, Munich, Germany
| | - Martin Vu
- Institute of Virology, Helmholtz Center Munich, Technical University of Munich (TUM), School of Medicine, Munich, Germany
| | - Kathrin Tinnefeld
- Institute of Virology, Helmholtz Center Munich, Technical University of Munich (TUM), School of Medicine, Munich, Germany
| | - Jochen Wettengel
- German Centre for Infection Research (DZIF), Partner Site, Munich, Germany.,Institute of Virology, Helmholtz Center Munich, Technical University of Munich (TUM), School of Medicine, Munich, Germany
| | - Dieter Hoffmann
- German Centre for Infection Research (DZIF), Partner Site, Munich, Germany.,Institute of Virology, Helmholtz Center Munich, Technical University of Munich (TUM), School of Medicine, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.,German Centre for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Christopher Daechert
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Helga Mairhofer
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Volker Fingerle
- Bavarian Health and Food Safety Authority (LGL (LGL), Oberschleißheim, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Philipp Steininger
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Veit Hornung
- Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Bernhard Liebl
- Bavarian Health and Food Safety Authority (LGL (LGL), Oberschleißheim, Germany
| | - Klaus Überla
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Martina Prelog
- Pediatric Rheumatology / Special Immunology, Pediatrics Department, University Hospital Würzburg, Würzburg, Germany
| | - Percy Knolle
- Institute of Molecular Immunology and Experimental Oncology, University Hospital rechts der Isar, Technical University of Munich (TUM), School of Medicine, Munich, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany. .,German Centre for Infection Research (DZIF), Partner Site, Munich, Germany.
| | - Ulrike Protzer
- German Centre for Infection Research (DZIF), Partner Site, Munich, Germany. .,Institute of Virology, Helmholtz Center Munich, Technical University of Munich (TUM), School of Medicine, Munich, Germany.
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Kerbs P, Vosberg S, Krebs S, Graf A, Blum H, Swoboda A, Batcha AMN, Mansmann U, Metzler D, Heckman CA, Herold T, Greif PA. Fusion gene detection by RNA-sequencing complements diagnostics of acute myeloid leukemia and identifies recurring NRIP1-MIR99AHG rearrangements. Haematologica 2022; 107:100-111. [PMID: 34134471 PMCID: PMC8719081 DOI: 10.3324/haematol.2021.278436] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 01/26/2021] [Accepted: 05/03/2021] [Indexed: 12/04/2022] Open
Abstract
Identification of fusion genes in clinical routine is mostly based on cytogenetics and targeted molecular genetics, such as metaphase karyotyping, fluorescence in situ hybridization and reverse-transcriptase polymerase chain reaction. However, sequencing technologies are becoming more important in clinical routine as processing time and costs per sample decrease. To evaluate the performance of fusion gene detection by RNAsequencing compared to standard diagnostic techniques, we analyzed 806 RNA-sequencing samples from patients with acute myeloid leukemia using two state-of-the-art software tools, namely Arriba and FusionCatcher. RNA-sequencing detected 90% of fusion events that were reported by routine with high evidence, while samples in which RNA-sequencing failed to detect fusion genes had overall lower and inhomogeneous sequence coverage. Based on properties of known and unknown fusion events, we developed a workflow with integrated filtering strategies for the identification of robust fusion gene candidates by RNA-sequencing. Thereby, we detected known recurrent fusion events in 26 cases that were not reported by routine and found discrepancies in evidence for known fusion events between routine and RNA-sequencing in three cases. Moreover, we identified 157 fusion genes as novel robust candidates and comparison to entries from ChimerDB or Mitelman Database showed novel recurrence of fusion genes in 14 cases. Finally, we detected the novel recurrent fusion gene NRIP1- MIR99AHG resulting from inv(21)(q11.2;q21.1) in nine patients (1.1%) and LTN1-MX1 resulting from inv(21)(q21.3;q22.3) in two patients (0.25%). We demonstrated that NRIP1-MIR99AHG results in overexpression of the 3' region of MIR99AHG and the disruption of the tricistronic miRNA cluster miR-99a/let-7c/miR-125b-2. Interestingly, upregulation of MIR99AHG and deregulation of the miRNA cluster, residing in the MIR99AHG locus, are known mechanisms of leukemogenesis in acute megakaryoblastic leukemia. Our findings demonstrate that RNA-sequencing has a strong potential to improve the systematic detection of fusion genes in clinical applications and provides a valuable tool for fusion discovery.
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Affiliation(s)
- Paul Kerbs
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Vosberg
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Anja Swoboda
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Aarif M N Batcha
- Department of Medical Data Processing, Biometry and Epidemiology, LMU Munich, Munich, Germany
| | - Ulrich Mansmann
- Department of Medical Data Processing, Biometry and Epidemiology, LMU Munich, Munich, Germany
| | - Dirk Metzler
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Caroline A Heckman
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp A Greif
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany.
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40
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Haebe S, Keay W, Alig S, Mohr AW, Martin LK, Heide M, Secci R, Krebs S, Blum H, Moosmann A, Louissaint A, Weinstock DM, Thoene S, von Bergwelt-Baildon M, Ruland J, Bararia D, Weigert O. The molecular ontogeny of follicular lymphoma: gene mutations succeeding the BCL2 translocation define common precursor cells. Br J Haematol 2021; 196:1381-1387. [PMID: 34967008 DOI: 10.1111/bjh.17990] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/23/2021] [Indexed: 11/29/2022]
Abstract
Relapsed follicular lymphoma (FL) can arise from common progenitor cells (CPCs). Conceptually, CPC-defining mutations are somatic alterations shared by the initial and relapsed tumours, mostly B-cell leukaemia/lymphoma 2 (BCL2)/immunoglobulin heavy locus (IGH) translocations and other recurrent gene mutations. Through complementary approaches for highly sensitive mutation detection, we do not find CPC-defining mutations in highly purified BCL2/IGH-negative haematopoietic progenitor cells in clinical remission samples from three patients with relapsed FL. Instead, we find cells harbouring the same BCL2/IGH translocation but lacking CREB binding protein (CREBBP), lysine methyltransferase 2D (KMT2D) and other recurrent gene mutations. Thus, (i) the BCL2/IGH translocation can precede CPC-defining mutations in human FL, and (ii) BCL2/IGH-translocated cells can persist in clinical remission.
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Affiliation(s)
- Sarah Haebe
- Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Hospital of the Ludwig-Maximilians-University (LMU), Munich, Germany.,Department of Medicine III, Hospital of the Ludwig-Maximilians-University (LMU), Munich, Germany
| | - William Keay
- Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Hospital of the Ludwig-Maximilians-University (LMU), Munich, Germany.,Department of Medicine III, Hospital of the Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Stefan Alig
- Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Hospital of the Ludwig-Maximilians-University (LMU), Munich, Germany.,Department of Medicine III, Hospital of the Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Anne-Wiebe Mohr
- Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit Gene Vectors, Munich, Germany
| | - Larissa K Martin
- Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit Gene Vectors, Munich, Germany
| | - Michael Heide
- Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Hospital of the Ludwig-Maximilians-University (LMU), Munich, Germany.,Department of Medicine III, Hospital of the Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Ramona Secci
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-University (LMU) of Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-University (LMU) of Munich, Munich, Germany
| | - Andreas Moosmann
- Department of Medicine III, Hospital of the Ludwig-Maximilians-University (LMU), Munich, Germany.,DZIF Research Group Host Control of Viral Latency and Reactivation, DZIF - German Center for Infection Research, Munich, Germany
| | - Abner Louissaint
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David M Weinstock
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Silvia Thoene
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael von Bergwelt-Baildon
- Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Hospital of the Ludwig-Maximilians-University (LMU), Munich, Germany.,Department of Medicine III, Hospital of the Ludwig-Maximilians-University (LMU), Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jürgen Ruland
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Deepak Bararia
- Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Hospital of the Ludwig-Maximilians-University (LMU), Munich, Germany.,Department of Medicine III, Hospital of the Ludwig-Maximilians-University (LMU), Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Weigert
- Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Hospital of the Ludwig-Maximilians-University (LMU), Munich, Germany.,Department of Medicine III, Hospital of the Ludwig-Maximilians-University (LMU), Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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41
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Penkava J, Muenchhoff M, Badell I, Osterman A, Delbridge C, Niederbuchner F, Soliman S, Rudelius M, Graf A, Krebs S, Blum H, Ulbig M, Baumann C, Zapp D, Maier M, Keppler OT, Lohmann CP, Ledderose S. Detection of SARS-CoV-2-RNA in post-mortem samples of human eyes. Graefes Arch Clin Exp Ophthalmol 2021; 260:1789-1797. [PMID: 34962592 PMCID: PMC8713040 DOI: 10.1007/s00417-021-05529-x] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/16/2021] [Accepted: 12/16/2021] [Indexed: 01/08/2023] Open
Abstract
Purpose To detect SARS-CoV-2 RNA in post-mortem human eyes. Ocular symptoms are common in patients with COVID-19. In some cases, they can occur before the onset of respiratory and other symptoms. Accordingly, SARS-CoV-2 RNA has been detected in conjunctival samples and tear film of patients suffering from COVID-19. However, the detection and clinical relevance of intravitreal SARS-CoV-2 RNA still remain unclear due to so far contradictory reports in the literature. Methods In our study 20 patients with confirmed diagnosis of COVID-19 were evaluated post-mortem to assess the conjunctival and intraocular presence of SARS-CoV-2 RNA using sterile pulmonary and conjunctival swabs as well as intravitreal biopsies (IVB) via needle puncture. SARS-CoV-2 PCR and whole genome sequencing from the samples of the deceased patients were performed. Medical history and comorbidities of all subjects were recorded and analyzed for correlations with viral data. Results SARS-CoV-2 RNA was detected in 10 conjunctival (50%) and 6 vitreal (30%) samples. SARS-CoV-2 whole genome sequencing showed the distribution of cases largely reflecting the frequency of circulating lineages in the Munich area at the time of examination with no preponderance of specific variants. Especially there was no association between the presence of SARS-CoV-2 RNA in IVBs and infection with the variant of concern (VOC) alpha. Viral load in bronchial samples correlated positively with load in conjunctiva but not the vitreous. Conclusion SARS-CoV-2 RNA can be detected post mortem in conjunctival tissues and IVBs. This is relevant to the planning of ophthalmologic surgical procedures in COVID-19 patients, such as pars plana vitrectomy or corneal transplantation. Furthermore, not only during surgery but also in an outpatient setting it is important to emphasize the need for personal protection in order to avoid infection and spreading of SARS-CoV-2. Prospective studies are needed, especially to determine the clinical relevance of conjunctival and intravitreal SARS-CoV-2 detection concerning intraocular affection in active COVID-19 state and in post-COVID syndrome.
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Affiliation(s)
- Josef Penkava
- Department of Ophthalmology, Technical University Munich, Munich, Germany.
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research, Partner Site Munich, Munich, Germany
| | - Irina Badell
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Andreas Osterman
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Claire Delbridge
- Department of Pathology and Neuropathology, TUM School of Medicine, Technical University Munich, Munich, Germany
| | | | - Sarah Soliman
- Department of Pathology, Ludwig-Maximilian University Munich, Munich, Germany
| | - Martina Rudelius
- Department of Pathology, Ludwig-Maximilian University Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-University, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-University, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-University, Munich, Germany
| | - Michael Ulbig
- Department of Ophthalmology, Technical University Munich, Munich, Germany
| | - Carmen Baumann
- Department of Ophthalmology, Technical University Munich, Munich, Germany
| | - Daniel Zapp
- Department of Ophthalmology, Technical University Munich, Munich, Germany
| | - Mathias Maier
- Department of Ophthalmology, Technical University Munich, Munich, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research, Partner Site Munich, Munich, Germany
| | - Chris P Lohmann
- Department of Ophthalmology, Technical University Munich, Munich, Germany
| | - Stephan Ledderose
- Department of Pathology, Ludwig-Maximilian University Munich, Munich, Germany
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42
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Flenkenthaler F, Ländström E, Shashikadze B, Backman M, Blutke A, Philippou-Massier J, Renner S, Hrabe de Angelis M, Wanke R, Blum H, Arnold GJ, Wolf E, Fröhlich T. Differential Effects of Insulin-Deficient Diabetes Mellitus on Visceral vs. Subcutaneous Adipose Tissue-Multi-omics Insights From the Munich MIDY Pig Model. Front Med (Lausanne) 2021; 8:751277. [PMID: 34888323 PMCID: PMC8650062 DOI: 10.3389/fmed.2021.751277] [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: 07/31/2021] [Accepted: 10/25/2021] [Indexed: 12/18/2022] Open
Abstract
Adipose tissue (AT) is no longer considered to be responsible for energy storage only but is now recognized as a major endocrine organ that is distributed across different parts of the body and is actively involved in regulatory processes controlling energy homeostasis. Moreover, AT plays a crucial role in the development of metabolic disease such as diabetes. Recent evidence has shown that adipokines have the ability to regulate blood glucose levels and improve metabolic homeostasis. While AT has been studied extensively in the context of type 2 diabetes, less is known about how different AT types are affected by absolute insulin deficiency in type 1 or permanent neonatal diabetes mellitus. Here, we analyzed visceral and subcutaneous AT in a diabetic, insulin-deficient pig model (MIDY) and wild-type (WT) littermate controls by RNA sequencing and quantitative proteomics. Multi-omics analysis indicates a depot-specific dysregulation of crucial metabolic pathways in MIDY AT samples. We identified key proteins involved in glucose uptake and downstream signaling, lipogenesis, lipolysis and β-oxidation to be differentially regulated between visceral and subcutaneous AT in response to insulin deficiency. Proteins related to glycogenolysis, pyruvate metabolism, TCA cycle and lipogenesis were increased in subcutaneous AT, whereas β-oxidation-related proteins were increased in visceral AT from MIDY pigs, pointing at a regionally different metabolic adaptation to master energy stress arising from diminished glucose utilization in MIDY AT. Chronic, absolute insulin deficiency and hyperglycemia revealed fat depot-specific signatures using multi-omics analysis. The generated datasets are a valuable resource for further comparative and translational studies in clinical diabetes research.
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Affiliation(s)
- Florian Flenkenthaler
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany.,German Center for Diabetes Research (DZD), Oberschleißheim, Germany
| | - Erik Ländström
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany.,Gene Center, Graduate School of Quantitative Biosciences Munich (QBM), Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Bachuki Shashikadze
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Mattias Backman
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany.,Gene Center, Graduate School of Quantitative Biosciences Munich (QBM), Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Andreas Blutke
- Helmholtz Zentrum München, Institute of Experimental Genetics, Oberschleißheim, Germany
| | - Julia Philippou-Massier
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany.,German Center for Diabetes Research (DZD), Oberschleißheim, Germany
| | - Simone Renner
- German Center for Diabetes Research (DZD), Oberschleißheim, Germany.,Department of Veterinary Sciences, Gene Center, Institute for Molecular Animal Breeding and Biotechnology, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany.,Center for Innovative Medical Models (CiMM), Ludwig-Maximilians-Universität (LMU) Munich, Oberschleißheim, Germany
| | - Martin Hrabe de Angelis
- German Center for Diabetes Research (DZD), Oberschleißheim, Germany.,Helmholtz Zentrum München, Institute of Experimental Genetics, Technical University of Munich, Munich, Germany
| | - Rüdiger Wanke
- Center for Clinical Veterinary Medicine, Institute of Veterinary Pathology, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Georg J Arnold
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Eckhard Wolf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany.,German Center for Diabetes Research (DZD), Oberschleißheim, Germany.,Department of Veterinary Sciences, Gene Center, Institute for Molecular Animal Breeding and Biotechnology, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany.,Center for Innovative Medical Models (CiMM), Ludwig-Maximilians-Universität (LMU) Munich, Oberschleißheim, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
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Rubio-Acero R, Beyerl J, Muenchhoff M, Roth MS, Castelletti N, Paunovic I, Radon K, Springer B, Nagel C, Boehm B, Böhmer MM, Graf A, Blum H, Krebs S, Keppler OT, Osterman A, Khan ZN, Hoelscher M, Wieser A. Spatially resolved qualified sewage spot sampling to track SARS-CoV-2 dynamics in Munich - One year of experience. Sci Total Environ 2021; 797:149031. [PMID: 34346361 PMCID: PMC8294104 DOI: 10.1016/j.scitotenv.2021.149031] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/23/2021] [Accepted: 07/09/2021] [Indexed: 05/03/2023]
Abstract
Wastewater-based epidemiology (WBE) is a tool now increasingly proposed to monitor the SARS-CoV-2 burden in populations without the need for individual mass testing. It is especially interesting in metropolitan areas where spread can be very fast, and proper sewage systems are available for sampling with short flow times and thus little decay of the virus. We started in March 2020 to set up a once-a-week qualified spot sampling protocol in six different locations in Munich carefully chosen to contain primarily wastewater of permanent residential areas, rather than industry or hospitals. We used RT-PCR and sequencing to track the spread of SARS-CoV-2 in the Munich population with temporo-spatial resolution. The study became fully operational in mid-April 2020 and has been tracking SARS-CoV-2 RNA load weekly for one year. Sequencing of the isolated viral RNA was performed to obtain information about the presence and abundance of variants of concern in the Munich area over time. We demonstrate that the evolution of SARS-CoV-2 RNA loads (between <7.5 and 3874/ml) in these different areas within Munich correlates well with official seven day incidence notification data (between 0.0 and 327 per 100,000) obtained from the authorities within the respective region. Wastewater viral loads predicted the dynamic of SARS-CoV-2 local incidence about 3 weeks in advance of data based on respiratory swab analyses. Aligning with multiple different point-mutations characteristic for certain variants of concern, we could demonstrate the gradual increase of variant of concern B.1.1.7 in the Munich population beginning in January 2021, weeks before it became apparent in sequencing results of swabs samples taken from patients living in Munich. Overall, the study highlights the potential of WBE to monitor the SARS-CoV-2 pandemic, including the introduction of variants of concern in a local population.
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Affiliation(s)
- Raquel Rubio-Acero
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80802 Munich, Germany.
| | - Jessica Beyerl
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80802 Munich, Germany.
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU Munich, 80336 Munich, Germany; German Center for Infection Research (DZIF), partner site Munich, Germany.
| | | | - Noemi Castelletti
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80802 Munich, Germany.
| | - Ivana Paunovic
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80802 Munich, Germany.
| | - Katja Radon
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, 80336 Munich, Germany; Center for International Health, Ludwig-Maximilians-University, Munich, Germany.
| | - Bernd Springer
- Fire Department, Disaster Control, City of Munich, Germany.
| | | | | | - Merle M Böhmer
- Taskforce Infectiology, Department for Infectious Disease Epidemiology (TFI 2), Bavarian Health and Food Safety Authority, Oberschleissheim, Germany; Institute of Social Medicine and Health Systems Research, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University of Munich, Munich, Germany.
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University of Munich, Munich, Germany.
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University of Munich, Munich, Germany.
| | - Oliver T Keppler
- German Center for Infection Research (DZIF), partner site Munich, Germany; Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU Munich, 80336 Munich, Germany.
| | - Andreas Osterman
- German Center for Infection Research (DZIF), partner site Munich, Germany; Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU Munich, 80336 Munich, Germany.
| | - Zohaib Nisar Khan
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80802 Munich, Germany.
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80802 Munich, Germany; Center for International Health, Ludwig-Maximilians-University, Munich, Germany; German Center for Infection Research (DZIF), partner site Munich, Germany.
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80802 Munich, Germany; German Center for Infection Research (DZIF), partner site Munich, Germany.
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Muenchhoff M, Graf A, Krebs S, Quartucci C, Hasmann S, Hellmuth JC, Scherer C, Osterman A, Boehm S, Mandel C, Becker-Pennrich AS, Zoller M, Stubbe HC, Munker S, Munker D, Milger K, Gapp M, Schneider S, Ruhle A, Jocham L, Nicolai L, Pekayvaz K, Weinberger T, Mairhofer H, Khatamzas E, Hofmann K, Spaeth PM, Bender S, Kääb S, Zwissler B, Mayerle J, Behr J, von Bergwelt-Baildon M, Reincke M, Grabein B, Hinske CL, Blum H, Keppler OT. Genomic epidemiology reveals multiple introductions of SARS-CoV-2 followed by community and nosocomial spread, Germany, February to May 2020. ACTA ACUST UNITED AC 2021; 26. [PMID: 34713795 PMCID: PMC8555370 DOI: 10.2807/1560-7917.es.2021.26.43.2002066] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background In the SARS-CoV-2 pandemic, viral genomes are available at unprecedented speed, but spatio-temporal bias in genome sequence sampling precludes phylogeographical inference without additional contextual data. Aim We applied genomic epidemiology to trace SARS-CoV-2 spread on an international, national and local level, to illustrate how transmission chains can be resolved to the level of a single event and single person using integrated sequence data and spatio-temporal metadata. Methods We investigated 289 COVID-19 cases at a university hospital in Munich, Germany, between 29 February and 27 May 2020. Using the ARTIC protocol, we obtained near full-length viral genomes from 174 SARS-CoV-2-positive respiratory samples. Phylogenetic analyses using the Auspice software were employed in combination with anamnestic reporting of travel history, interpersonal interactions and perceived high-risk exposures among patients and healthcare workers to characterise cluster outbreaks and establish likely scenarios and timelines of transmission. Results We identified multiple independent introductions in the Munich Metropolitan Region during the first weeks of the first pandemic wave, mainly by travellers returning from popular skiing areas in the Alps. In these early weeks, the rate of presumable hospital-acquired infections among patients and in particular healthcare workers was high (9.6% and 54%, respectively) and we illustrated how transmission chains can be dissected at high resolution combining virus sequences and spatio-temporal networks of human interactions. Conclusions Early spread of SARS-CoV-2 in Europe was catalysed by superspreading events and regional hotspots during the winter holiday season. Genomic epidemiology can be employed to trace viral spread and inform effective containment strategies.
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Affiliation(s)
- Maximilian Muenchhoff
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Caroline Quartucci
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Sandra Hasmann
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany
| | - Johannes C Hellmuth
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Clemens Scherer
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Andreas Osterman
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Stephan Boehm
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Christopher Mandel
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany
| | - Andrea Sabine Becker-Pennrich
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.,Department of Medical Information Processing, Biometry and Epidemiology (IBE), LMU Munich, Munich, Germany
| | - Michael Zoller
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Hans Christian Stubbe
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Stefan Munker
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Dieter Munker
- Department of Medicine V, University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Katrin Milger
- Department of Medicine V, University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Madeleine Gapp
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Stephanie Schneider
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Adrian Ruhle
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Linda Jocham
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Leo Nicolai
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Kami Pekayvaz
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Tobias Weinberger
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Helga Mairhofer
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Elham Khatamzas
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Katharina Hofmann
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia M Spaeth
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Sabine Bender
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Stefan Kääb
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Bernhard Zwissler
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Julia Mayerle
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Juergen Behr
- Department of Medicine V, University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Michael von Bergwelt-Baildon
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Martin Reincke
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.,Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany
| | - Beatrice Grabein
- Department of Clinical Microbiology and Hospital Hygiene, University Hospital, LMU Munich, Munich, Germany
| | - Christian Ludwig Hinske
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.,Department of Medical Information Processing, Biometry and Epidemiology (IBE), LMU Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
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Upadhyay M, Kunz E, Sandoval-Castellanos E, Hauser A, Krebs S, Graf A, Blum H, Dotsev A, Okhlopkov I, Shakhin A, Bagirov V, Brem G, Fries R, Zinovieva N, Medugorac I. Whole genome sequencing reveals a complex introgression history and the basis of adaptation to subarctic climate in wild sheep. Mol Ecol 2021; 30:6701-6717. [PMID: 34534381 DOI: 10.1111/mec.16184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/01/2021] [Accepted: 09/07/2021] [Indexed: 11/29/2022]
Abstract
To predict species responses to anthropogenic disturbances and climate change, it is reasonable to use species with high sensitivity to such factors. Snow sheep (Ovis nivicola) could represent a good candidate for this; as the only large herbivore species adapted to the cold and alpine habitats of northeastern Siberia, it plays a crucial role in its ecosystem. Despite having an extensive geographical distribution among all ovine species, it is one of the least studied. In this study, we sequenced and analysed six genomes of snow sheep in combination with all other wild sheep species to infer key aspects of their evolutionary history and unveil the genetic basis of their adaptation to subarctic environments. Despite their large census population size, snow sheep genomes showed remarkably low heterozygosity, which could reflect the effect of isolation and historical bottlenecks that we inferred using the pairwise sequential Markovian coalescent and runs of homozygosity. F4 -statistics indicated instances of introgression involving snow sheep with argali (Ovis ammon) and Dall (Ovis dalli) sheep, suggesting that these species might have been more widespread during the Pleistocene. Furthermore, the introgressed segments, which were identified using mainly minimum relative node depth, covered genes associated with immunity, adipogenesis and morphology-related traits, representing potential targets of adaptive introgression. Genes related to mitochondrial functions and thermogenesis associated with adipose tissue were identified to be under selection. Overall, our data suggest introgression as a mechanism facilitating adaptation in wild sheep species and provide insights into the genetic mechanisms underlying cold adaptation in snow sheep.
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Affiliation(s)
- Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Elisabeth Kunz
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | | | - Andreas Hauser
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Arsen Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | | | - Alexey Shakhin
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | - Vugar Bagirov
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, VMU, Vienna, Austria
| | - Ruedi Fries
- Lehrstuhl für Tierzucht, Technische Universität München, Freising, Germany
| | - Natalia Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
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Osterman A, Iglhaut M, Lehner A, Späth P, Stern M, Autenrieth H, Muenchhoff M, Graf A, Krebs S, Blum H, Baiker A, Grzimek-Koschewa N, Protzer U, Kaderali L, Baldauf HM, Keppler OT. Comparison of four commercial, automated antigen tests to detect SARS-CoV-2 variants of concern. Med Microbiol Immunol 2021; 210:263-275. [PMID: 34415422 PMCID: PMC8377707 DOI: 10.1007/s00430-021-00719-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 08/08/2021] [Accepted: 08/13/2021] [Indexed: 12/23/2022]
Abstract
A versatile portfolio of diagnostic tests is essential for the containment of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) pandemic. Besides nucleic acid-based test systems and point-of-care (POCT) antigen (Ag) tests, quantitative, laboratory-based nucleocapsid Ag tests for SARS-CoV-2 have recently been launched. Here, we evaluated four commercial Ag tests on automated platforms and one POCT to detect SARS-CoV-2. We evaluated PCR-positive (n = 107) and PCR-negative (n = 303) respiratory swabs from asymptomatic and symptomatic patients at the end of the second pandemic wave in Germany (February–March 2021) as well as clinical isolates EU1 (B.1.117), variant of concern (VOC) Alpha (B.1.1.7) or Beta (B.1.351), which had been expanded in a biosafety level 3 laboratory. The specificities of automated SARS-CoV-2 Ag tests ranged between 97.0 and 99.7% (Lumipulse G SARS-CoV-2 Ag (Fujirebio): 97.03%, Elecsys SARS-CoV-2 Ag (Roche Diagnostics): 97.69%; LIAISON® SARS-CoV-2 Ag (Diasorin) and SARS-CoV-2 Ag ELISA (Euroimmun): 99.67%). In this study cohort of hospitalized patients, the clinical sensitivities of tests were low, ranging from 17.76 to 52.34%, and analytical sensitivities ranged from 420,000 to 25,000,000 Geq/ml. In comparison, the detection limit of the Roche Rapid Ag Test (RAT) was 9,300,000 Geq/ml, detecting 23.58% of respiratory samples. Receiver-operating-characteristics (ROCs) and Youden’s index analyses were performed to further characterize the assays’ overall performance and determine optimal assay cutoffs for sensitivity and specificity. VOCs carrying up to four amino acid mutations in nucleocapsid were detected by all five assays with characteristics comparable to non-VOCs. In summary, automated, quantitative SARS-CoV-2 Ag tests show variable performance and are not necessarily superior to a standard POCT. The efficacy of any alternative testing strategies to complement nucleic acid-based assays must be carefully evaluated by independent laboratories prior to widespread implementation.
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Affiliation(s)
- Andreas Osterman
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Iglhaut
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Andreas Lehner
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia Späth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Marcel Stern
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Hanna Autenrieth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Armin Baiker
- Public Health Microbiology Unit, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Natascha Grzimek-Koschewa
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Ulrike Protzer
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Hanna-Mari Baldauf
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- Max Von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany.
| | - Oliver T Keppler
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany.
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.
- Max Von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany.
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47
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Buschle A, Mrozek-Gorska P, Cernilogar FM, Ettinger A, Pich D, Krebs S, Mocanu B, Blum H, Schotta G, Straub T, Hammerschmidt W. Epstein-Barr virus inactivates the transcriptome and disrupts the chromatin architecture of its host cell in the first phase of lytic reactivation. Nucleic Acids Res 2021; 49:3217-3241. [PMID: 33675667 PMCID: PMC8034645 DOI: 10.1093/nar/gkab099] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/01/2021] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus (EBV), a herpes virus also termed HHV 4 and the first identified human tumor virus, establishes a stable, long-term latent infection in human B cells, its preferred host. Upon induction of EBV's lytic phase, the latently infected cells turn into a virus factory, a process that is governed by EBV. In the lytic, productive phase, all herpes viruses ensure the efficient induction of all lytic viral genes to produce progeny, but certain of these genes also repress the ensuing antiviral responses of the virally infected host cells, regulate their apoptotic death or control the cellular transcriptome. We now find that EBV causes previously unknown massive and global alterations in the chromatin of its host cell upon induction of the viral lytic phase and prior to the onset of viral DNA replication. The viral initiator protein of the lytic cycle, BZLF1, binds to >105 binding sites with different sequence motifs in cellular chromatin in a concentration dependent manner implementing a binary molar switch probably to prevent noise-induced erroneous induction of EBV's lytic phase. Concomitant with DNA binding of BZLF1, silent chromatin opens locally as shown by ATAC-seq experiments, while previously wide-open cellular chromatin becomes inaccessible on a global scale within hours. While viral transcripts increase drastically, the induction of the lytic phase results in a massive reduction of cellular transcripts and a loss of chromatin-chromatin interactions of cellular promoters with their distal regulatory elements as shown in Capture-C experiments. Our data document that EBV's lytic cycle induces discrete early processes that disrupt the architecture of host cellular chromatin and repress the cellular epigenome and transcriptome likely supporting the efficient de novo synthesis of this herpes virus.
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Affiliation(s)
- Alexander Buschle
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health and German Center for Infection Research (DZIF), Partner site Munich, Germany, Feodor-Lynen-Str. 21, D-81377 Munich, Germany
| | - Paulina Mrozek-Gorska
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health and German Center for Infection Research (DZIF), Partner site Munich, Germany, Feodor-Lynen-Str. 21, D-81377 Munich, Germany
| | - Filippo M Cernilogar
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität (LMU) München, 82152 Planegg-Martinsried, Germany
| | - Andreas Ettinger
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health, Feodor-Lynen-Str. 21 D-81377 Munich, Germany
| | - Dagmar Pich
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health and German Center for Infection Research (DZIF), Partner site Munich, Germany, Feodor-Lynen-Str. 21, D-81377 Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center of the Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Bianca Mocanu
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health and German Center for Infection Research (DZIF), Partner site Munich, Germany, Feodor-Lynen-Str. 21, D-81377 Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center of the Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany
| | - Gunnar Schotta
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität (LMU) München, 82152 Planegg-Martinsried, Germany
| | - Tobias Straub
- Bioinformatics Unit, Biomedical Center, Ludwig-Maximilians-Universität (LMU) München, 82152 Planegg-Martinsried, Germany
| | - Wolfgang Hammerschmidt
- Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health and German Center for Infection Research (DZIF), Partner site Munich, Germany, Feodor-Lynen-Str. 21, D-81377 Munich, Germany
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48
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Kirstein N, Buschle A, Wu X, Krebs S, Blum H, Kremmer E, Vorberg IM, Hammerschmidt W, Lacroix L, Hyrien O, Audit B, Schepers A. Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zones. eLife 2021; 10:62161. [PMID: 33683199 PMCID: PMC7993996 DOI: 10.7554/elife.62161] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 08/16/2020] [Accepted: 03/05/2021] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic DNA replication initiates during S phase from origins that have been licensed in the preceding G1 phase. Here, we compare ChIP-seq profiles of the licensing factors Orc2, Orc3, Mcm3, and Mcm7 with gene expression, replication timing, and fork directionality profiles obtained by RNA-seq, Repli-seq, and OK-seq. Both, the origin recognition complex (ORC) and the minichromosome maintenance complex (MCM) are significantly and homogeneously depleted from transcribed genes, enriched at gene promoters, and more abundant in early- than in late-replicating domains. Surprisingly, after controlling these variables, no difference in ORC/MCM density is detected between initiation zones, termination zones, unidirectionally replicating regions, and randomly replicating regions. Therefore, ORC/MCM density correlates with replication timing but does not solely regulate the probability of replication initiation. Interestingly, H4K20me3, a histone modification proposed to facilitate late origin licensing, was enriched in late-replicating initiation zones and gene deserts of stochastic replication fork direction. We discuss potential mechanisms specifying when and where replication initiates in human cells.
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Affiliation(s)
- Nina Kirstein
- Research Unit Gene Vectors, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health, Munich, Germany
| | - Alexander Buschle
- Research Unit Gene Vectors, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health and German Center for Infection Research (DZIF), Munich, Germany
| | - Xia Wu
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center of the Ludwig-Maximilians Universität (LMU) München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center of the Ludwig-Maximilians Universität (LMU) München, Munich, Germany
| | - Elisabeth Kremmer
- Institute for Molecular Immunology, Monoclonal Antibody Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Ina M Vorberg
- German Center for Neurodegenerative Diseases (DZNE e.V.), Bonn, Germany.,Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Wolfgang Hammerschmidt
- Research Unit Gene Vectors, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health and German Center for Infection Research (DZIF), Munich, Germany
| | - Laurent Lacroix
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Olivier Hyrien
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Benjamin Audit
- Univ Lyon, ENS de Lyon, Univ. Claude Bernard, CNRS, Laboratoire de Physique, 69342 Lyon, France
| | - Aloys Schepers
- Research Unit Gene Vectors, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health, Munich, Germany
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Weinberger T, Steffen J, Osterman A, Mueller TT, Muenchhoff M, Wratil PR, Graf A, Krebs S, Quartucci C, Spaeth PM, Grabein B, Adorjan K, Blum H, Keppler OT, Klein M. Prospective Longitudinal Serosurvey of Health Care Workers in the First Wave of the SARS-CoV-2 Pandemic in a Quaternary Care Hospital in Munich, Germany. Clin Infect Dis 2021; 73:e3055-e3065. [PMID: 33388756 PMCID: PMC7799305 DOI: 10.1093/cid/ciaa1935] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Indexed: 12/26/2022] Open
Abstract
Background High infection rates among health care personnel in an uncontained pandemic can paralyze health systems due to staff shortages. Risk constellations and rates of seroconversion for health care workers during the first wave of the SARS-CoV-2 pandemic are still largely unclear. Methods Health care personnel (n=300) on different organizational units in the LMU Munich University Hospital were included and followed in this prospective longitudinal study in the period of March 24 until July 7, 2020. Participants were monitored in intervals of two to six weeks using different antibody assays for serological testing and questionnaires to evaluate risk contacts. In a subgroup of infected participants, we obtained nasopharyngeal swabs to perform whole genome sequencing for outbreak characterization. Results Health care workers involved in patient care on dedicated COVID-19 wards or on regular non-COVID-19 wards showed a higher rate of SARS-CoV-2 seroconversion compared to staff in the emergency department and non-frontline personnel. The landscape of risk contacts in these units was dynamic, with a decrease of unprotected risk contacts in the emergency department and an increase on non-COVID-19 wards. Both, the intensity and number of risk contacts, were associated with higher rates of seroconversion. On regular wards, staff infections tended to occur in clusters, while infections on COVID-19 wards were less frequent and apparently independent of each other. Conclusion The risk of SARS-CoV-2 infection for front-line health care workers was increased during the first pandemic wave in Southern Germany. Stringent measures for infection control are essential to protect all patient-facing staff during the ongoing pandemic.
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Affiliation(s)
- Tobias Weinberger
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Julius Steffen
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Andreas Osterman
- Max von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Germany
| | - Tonina T Mueller
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich
| | - Paul R Wratil
- Max von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilian University of Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilian University of Munich, Munich, Germany
| | - Carolina Quartucci
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, LMU München, Munich, Germany
| | - Patricia M Spaeth
- Max von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Germany
| | - Beatrice Grabein
- Department for Clinical Microbiology and Hospital Hygiene, LMU Munich, Munich, Germany
| | - Kristina Adorjan
- Department of Psychiatry and Psychotherapy, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilian University of Munich, Munich, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Germany
| | - Matthias Klein
- Emergency Department, University Hospital, LMU Munich, Munich, Germany.,Department of Neurology, University Hospital, LMU Munich, Munich, Germany
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Panagiotopoulos AL, Karguth N, Pavlou M, Böhm S, Gasparoni G, Walter J, Graf A, Blum H, Biel M, Riedmayr LM, Becirovic E. Antisense Oligonucleotide- and CRISPR-Cas9-Mediated Rescue of mRNA Splicing for a Deep Intronic CLRN1 Mutation. Mol Ther Nucleic Acids 2020; 21:1050-1061. [PMID: 32841912 PMCID: PMC7452116 DOI: 10.1016/j.omtn.2020.07.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/23/2020] [Accepted: 07/27/2020] [Indexed: 12/26/2022]
Abstract
Mutations in CLRN1 cause Usher syndrome (USH) type III (USH3A), a disease characterized by progressive hearing impairment, retinitis pigmentosa, and vestibular dysfunction. Due to the lack of appropriate disease models, no efficient therapy for retinitis pigmentosa in USH patients exists so far. In addition, given the yet undefined functional role and expression of the different CLRN1 splice isoforms in the retina, non-causative therapies such as gene supplementation are unsuitable at this stage. In this study, we focused on the recently identified deep intronic c.254-649T>G CLRN1 splicing mutation and aimed to establish two causative treatment approaches: CRISPR-Cas9-mediated excision of the mutated intronic region and antisense oligonucleotide (AON)-mediated correction of mRNA splicing. The therapeutic potential of these approaches was validated in different cell types transiently or stably expressing CLRN1 minigenes. Both approaches led to substantial correction of the splice defect. Surprisingly, however, no synergistic effect was detected when combining both methods. Finally, the injection of naked AONs into mice expressing the mutant CLRN1 minigene in the retina also led to a significant splice rescue. We propose that both AONs and CRISPR-Cas9 are suitable strategies to initiate advanced preclinical studies for treatment of USH3A patients.
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Affiliation(s)
- Anna-Lena Panagiotopoulos
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nina Karguth
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany; Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marina Pavlou
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany; Department of Ophthalmology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sybille Böhm
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany; Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gilles Gasparoni
- Department of Genetics, Saarland University, Saarbrücken, Germany
| | - Jörn Walter
- Department of Genetics, Saarland University, Saarbrücken, Germany
| | - Alexander Graf
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Helmut Blum
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Martin Biel
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany; Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lisa Maria Riedmayr
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany; Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Elvir Becirovic
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany; Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany.
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