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Gündüz HA, Mreches R, Moosbauer J, Robertson G, To XY, Franzosa EA, Huttenhower C, Rezaei M, McHardy AC, Bischl B, Münch PC, Binder M. Optimized model architectures for deep learning on genomic data. Commun Biol 2024; 7:516. [PMID: 38693292 PMCID: PMC11063068 DOI: 10.1038/s42003-024-06161-1] [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: 02/08/2023] [Accepted: 04/08/2024] [Indexed: 05/03/2024] Open
Abstract
The success of deep learning in various applications depends on task-specific architecture design choices, including the types, hyperparameters, and number of layers. In computational biology, there is no consensus on the optimal architecture design, and decisions are often made using insights from more well-established fields such as computer vision. These may not consider the domain-specific characteristics of genome sequences, potentially limiting performance. Here, we present GenomeNet-Architect, a neural architecture design framework that automatically optimizes deep learning models for genome sequence data. It optimizes the overall layout of the architecture, with a search space specifically designed for genomics. Additionally, it optimizes hyperparameters of individual layers and the model training procedure. On a viral classification task, GenomeNet-Architect reduced the read-level misclassification rate by 19%, with 67% faster inference and 83% fewer parameters, and achieved similar contig-level accuracy with ~100 times fewer parameters compared to the best-performing deep learning baselines.
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Affiliation(s)
- Hüseyin Anil Gündüz
- Department of Statistics, LMU Munich, Munich, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - René Mreches
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Julia Moosbauer
- Department of Statistics, LMU Munich, Munich, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - Gary Robertson
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Xiao-Yin To
- Department of Statistics, LMU Munich, Munich, Germany
- Munich Center for Machine Learning, Munich, Germany
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Eric A Franzosa
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Mina Rezaei
- Department of Statistics, LMU Munich, Munich, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - Alice C McHardy
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
- German Centre for Infection Research (DZIF), partner site Hannover Braunschweig, Braunschweig, Germany
| | - Bernd Bischl
- Department of Statistics, LMU Munich, Munich, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - Philipp C Münch
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany.
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
- German Centre for Infection Research (DZIF), partner site Hannover Braunschweig, Braunschweig, Germany.
| | - Martin Binder
- Department of Statistics, LMU Munich, Munich, Germany.
- Munich Center for Machine Learning, Munich, Germany.
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Muecksch F, Fackler OT. Eliciting CD4-mimicking broadly neutralizing antibodies: new avenues towards the rational design of an HIV vaccine. Signal Transduct Target Ther 2024; 9:49. [PMID: 38424414 PMCID: PMC10904788 DOI: 10.1038/s41392-024-01776-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/06/2024] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Affiliation(s)
- Frauke Muecksch
- Department of Infectious Diseases, Heidelberg University, Medical Faculty Heidelberg, Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg, Germany
- Chica and Heinz Schaller (CHS) Research Group, Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Oliver T Fackler
- Department of Infectious Diseases, Heidelberg University, Medical Faculty Heidelberg, Integrative Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg, Germany.
- German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany.
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3
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Frenz-Wiessner S, Fairley SD, Buser M, Goek I, Salewskij K, Jonsson G, Illig D, Zu Putlitz B, Petersheim D, Li Y, Chen PH, Kalauz M, Conca R, Sterr M, Geuder J, Mizoguchi Y, Megens RTA, Linder MI, Kotlarz D, Rudelius M, Penninger JM, Marr C, Klein C. Generation of complex bone marrow organoids from human induced pluripotent stem cells. Nat Methods 2024:10.1038/s41592-024-02172-2. [PMID: 38374263 DOI: 10.1038/s41592-024-02172-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 01/09/2024] [Indexed: 02/21/2024]
Abstract
The human bone marrow (BM) niche sustains hematopoiesis throughout life. We present a method for generating complex BM-like organoids (BMOs) from human induced pluripotent stem cells (iPSCs). BMOs consist of key cell types that self-organize into spatially defined three-dimensional structures mimicking cellular, structural and molecular characteristics of the hematopoietic microenvironment. Functional properties of BMOs include the presence of an in vivo-like vascular network, the presence of multipotent mesenchymal stem/progenitor cells, the support of neutrophil differentiation and responsiveness to inflammatory stimuli. Single-cell RNA sequencing revealed a heterocellular composition including the presence of a hematopoietic stem/progenitor (HSPC) cluster expressing genes of fetal HSCs. BMO-derived HSPCs also exhibited lymphoid potential and a subset demonstrated transient engraftment potential upon xenotransplantation in mice. We show that the BMOs could enable the modeling of hematopoietic developmental aspects and inborn errors of hematopoiesis, as shown for human VPS45 deficiency. Thus, iPSC-derived BMOs serve as a physiologically relevant in vitro model of the human BM microenvironment to study hematopoietic development and BM diseases.
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Affiliation(s)
- Stephanie Frenz-Wiessner
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Savannah D Fairley
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
- Institute of Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University Munich, Munich, Germany
| | - Maximilian Buser
- Institute of AI for Health, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Isabel Goek
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Kirill Salewskij
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Gustav Jonsson
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - David Illig
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Benedicta Zu Putlitz
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Daniel Petersheim
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Yue Li
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Pin-Hsuan Chen
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Martina Kalauz
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Raffaele Conca
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, 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
- Technical University of Munich, Munich, Germany
| | - Johanna Geuder
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-University Munich, Martinsried, Germany
| | - Yoko Mizoguchi
- Department of Pediatrics, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Remco T A Megens
- Institute of Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University Munich, Munich, Germany
- Department of Biomedical Engineering (BME), Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, Maastricht, The Netherlands
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Monika I Linder
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Daniel Kotlarz
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Martina Rudelius
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
- Helmholtz Centre for Infection Research, Braunschweig, Germany
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Carsten Marr
- Institute of AI for Health, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany.
- Gene Center, Ludwig-Maximilians-University Munich, Munich, Germany.
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4
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Sake SM, Zhang X, Rajak MK, Urbanek-Quaing M, Carpentier A, Gunesch AP, Grethe C, Matthaei A, Rückert J, Galloux M, Larcher T, Le Goffic R, Hontonnou F, Chatterjee AK, Johnson K, Morwood K, Rox K, Elgaher WAM, Huang J, Wetzke M, Hansen G, Fischer N, Eléouët JF, Rameix-Welti MA, Hirsch AKH, Herold E, Empting M, Lauber C, Schulz TF, Krey T, Haid S, Pietschmann T. Drug repurposing screen identifies lonafarnib as respiratory syncytial virus fusion protein inhibitor. Nat Commun 2024; 15:1173. [PMID: 38332002 PMCID: PMC10853176 DOI: 10.1038/s41467-024-45241-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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/16/2024] [Indexed: 02/10/2024] Open
Abstract
Respiratory syncytial virus (RSV) is a common cause of acute lower respiratory tract infection in infants, older adults and the immunocompromised. Effective directly acting antivirals are not yet available for clinical use. To address this, we screen the ReFRAME drug-repurposing library consisting of 12,000 small molecules against RSV. We identify 21 primary candidates including RSV F and N protein inhibitors, five HSP90 and four IMPDH inhibitors. We select lonafarnib, a licensed farnesyltransferase inhibitor, and phase III candidate for hepatitis delta virus (HDV) therapy, for further follow-up. Dose-response analyses and plaque assays confirm the antiviral activity (IC50: 10-118 nM). Passaging of RSV with lonafarnib selects for phenotypic resistance and fixation of mutations in the RSV fusion protein (T335I and T400A). Lentiviral pseudotypes programmed with variant RSV fusion proteins confirm that lonafarnib inhibits RSV cell entry and that these mutations confer lonafarnib resistance. Surface plasmon resonance reveals RSV fusion protein binding of lonafarnib and co-crystallography identifies the lonafarnib binding site within RSV F. Oral administration of lonafarnib dose-dependently reduces RSV virus load in a murine infection model using female mice. Collectively, this work provides an overview of RSV drug repurposing candidates and establishes lonafarnib as a bona fide fusion protein inhibitor.
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Affiliation(s)
- Svenja M Sake
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Xiaoyu Zhang
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Manoj Kumar Rajak
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, Luebeck, Germany
| | - Melanie Urbanek-Quaing
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Arnaud Carpentier
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Antonia P Gunesch
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Christina Grethe
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Alina Matthaei
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Jessica Rückert
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Marie Galloux
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | | | - Ronan Le Goffic
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | | | | | | | | | - Katharina Rox
- Department of Chemical Biology, Helmholtz Center of Infection Research, Braunschweig, Germany
- German Centre for Infection Research, Partner site Braunschweig-Hannover, Braunschweig, Germany
| | - Walid A M Elgaher
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-HZI, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Jiabin Huang
- Insitute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Wetzke
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Partner Site Hannover, BREATH, Hannover, Germany
| | - Gesine Hansen
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Partner Site Hannover, BREATH, Hannover, Germany
| | - Nicole Fischer
- Insitute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Marie-Anne Rameix-Welti
- Université Paris-Saclay, Université de Versailles St. Quentin; UMR 1173 (2I), INSERM; Assistance Publique des Hôpitaux de Paris, Hôpital Ambroise Paré, Laboratoire de Microbiologie, DMU15, Versailles, France
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-HZI, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Helmholtz International Lab for Anti-infectives, HZI, Braunschweig, Germany
| | - Elisabeth Herold
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, Luebeck, Germany
| | - Martin Empting
- German Centre for Infection Research, Partner site Braunschweig-Hannover, Braunschweig, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-HZI, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Chris Lauber
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Thomas F Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Centre for Infection Research, Partner site Braunschweig-Hannover, Braunschweig, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Thomas Krey
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, Luebeck, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Luebeck-Borstel-Riems, Luebeck, Germany
| | - Sibylle Haid
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany.
| | - Thomas Pietschmann
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany.
- German Centre for Infection Research, Partner site Braunschweig-Hannover, Braunschweig, Germany.
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
- Helmholtz International Lab for Anti-infectives, HZI, Braunschweig, Germany.
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5
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Mayer L, Weskamm LM, Fathi A, Kono M, Heidepriem J, Krähling V, Mellinghoff SC, Ly ML, Friedrich M, Hardtke S, Borregaard S, Hesterkamp T, Loeffler FF, Volz A, Sutter G, Becker S, Dahlke C, Addo MM. MVA-based vaccine candidates encoding the native or prefusion-stabilized SARS-CoV-2 spike reveal differential immunogenicity in humans. NPJ Vaccines 2024; 9:20. [PMID: 38278816 PMCID: PMC10817990 DOI: 10.1038/s41541-023-00801-z] [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: 07/27/2023] [Accepted: 12/12/2023] [Indexed: 01/28/2024] Open
Abstract
In response to the COVID-19 pandemic, multiple vaccines were developed using platforms such as viral vectors and mRNA technology. Here, we report humoral and cellular immunogenicity data from human phase 1 clinical trials investigating two recombinant Modified Vaccinia virus Ankara vaccine candidates, MVA-SARS-2-S and MVA-SARS-2-ST, encoding the native and the prefusion-stabilized SARS-CoV-2 spike protein, respectively. MVA-SARS-2-ST was more immunogenic than MVA-SARS-2-S, but both were less immunogenic compared to licensed mRNA- and ChAd-based vaccines in SARS-CoV-2 naïve individuals. In heterologous vaccination, previous MVA-SARS-2-S vaccination enhanced T cell functionality and MVA-SARS-2-ST boosted the frequency of T cells and S1-specific IgG levels when used as a third vaccination. While the vaccine candidate containing the prefusion-stabilized spike elicited predominantly S1-specific responses, immunity to the candidate with the native spike was skewed towards S2-specific responses. These data demonstrate how the spike antigen conformation, using the same viral vector, directly affects vaccine immunogenicity in humans.
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Affiliation(s)
- Leonie Mayer
- Institute for Infection Research and Vaccine Development (IIRVD), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
- Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
- German Centre for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.
| | - Leonie M Weskamm
- Institute for Infection Research and Vaccine Development (IIRVD), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Centre for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Anahita Fathi
- Institute for Infection Research and Vaccine Development (IIRVD), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Centre for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- First Department of Medicine, Division of Infectious Diseases, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Maya Kono
- Institute for Infection Research and Vaccine Development (IIRVD), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Centre for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Jasmin Heidepriem
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Verena Krähling
- Institute for Virology, Philipps University Marburg, Marburg, Germany
- German Centre for Infection Research, Partner Site Gießen-Marburg-Langen, Marburg, Germany
| | - Sibylle C Mellinghoff
- Faculty of Medicine and University Hospital of Cologne, Department I of Internal Medicine, Centre for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), German CLL Group (GCLLSG), University of Cologne, Cologne, Germany
- German Centre for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - My Linh Ly
- Institute for Infection Research and Vaccine Development (IIRVD), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Centre for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Monika Friedrich
- Institute for Infection Research and Vaccine Development (IIRVD), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Centre for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Svenja Hardtke
- Institute for Infection Research and Vaccine Development (IIRVD), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Centre for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | | | - Thomas Hesterkamp
- German Centre for Infection Research, Translational Project Management Office, Brunswick, Germany
| | - Felix F Loeffler
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Asisa Volz
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
- German Centre for Infection Research, Partner Site Hannover-Brunswick, Hanover, Germany
| | - Gerd Sutter
- Division of Virology, Department of Veterinary Sciences, Institute for Infectious Diseases and Zoonoses, LMU Munich, Munich, Germany
- German Centre for Infection Research, Partner Site Munich, Munich, Germany
| | - Stephan Becker
- Institute for Virology, Philipps University Marburg, Marburg, Germany
- German Centre for Infection Research, Partner Site Gießen-Marburg-Langen, Marburg, Germany
| | - Christine Dahlke
- Institute for Infection Research and Vaccine Development (IIRVD), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Centre for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Marylyn M Addo
- Institute for Infection Research and Vaccine Development (IIRVD), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
- Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
- German Centre for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.
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6
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Giehler F, Ostertag MS, Sommermann T, Weidl D, Sterz KR, Kutz H, Moosmann A, Feller SM, Geerlof A, Biesinger B, Popowicz GM, Kirchmair J, Kieser A. Epstein-Barr virus-driven B cell lymphoma mediated by a direct LMP1-TRAF6 complex. Nat Commun 2024; 15:414. [PMID: 38195569 PMCID: PMC10776578 DOI: 10.1038/s41467-023-44455-w] [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: 01/25/2022] [Accepted: 12/14/2023] [Indexed: 01/11/2024] Open
Abstract
Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1) drives viral B cell transformation and oncogenesis. LMP1's transforming activity depends on its C-terminal activation region 2 (CTAR2), which induces NF-κB and JNK by engaging TNF receptor-associated factor 6 (TRAF6). The mechanism of TRAF6 recruitment to LMP1 and its role in LMP1 signalling remains elusive. Here we demonstrate that TRAF6 interacts directly with a viral TRAF6 binding motif within CTAR2. Functional and NMR studies supported by molecular modeling provide insight into the architecture of the LMP1-TRAF6 complex, which differs from that of CD40-TRAF6. The direct recruitment of TRAF6 to LMP1 is essential for NF-κB activation by CTAR2 and the survival of LMP1-driven lymphoma. Disruption of the LMP1-TRAF6 complex by inhibitory peptides interferes with the survival of EBV-transformed B cells. In this work, we identify LMP1-TRAF6 as a critical virus-host interface and validate this interaction as a potential therapeutic target in EBV-associated cancer.
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Affiliation(s)
- Fabian Giehler
- Research Unit Signaling and Translation, Helmholtz Center Munich - German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Research Unit Gene Vectors, Helmholtz Center Munich - German Research Center for Environmental Health, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Michael S Ostertag
- Institute of Structural Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Thomas Sommermann
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Daniel Weidl
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, 91054, Erlangen, Germany
| | - Kai R Sterz
- Research Unit Gene Vectors, Helmholtz Center Munich - German Research Center for Environmental Health, 81377, Munich, Germany
| | - Helmut Kutz
- Research Unit Gene Vectors, Helmholtz Center Munich - German Research Center for Environmental Health, 81377, Munich, Germany
| | - Andreas Moosmann
- Research Unit Gene Vectors, Helmholtz Center Munich - German Research Center for Environmental Health, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- Department of Medicine III, University Hospital, Ludwig-Maximilians-University Munich, 81377, Munich, Germany
| | - Stephan M Feller
- Institute of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, 06120, Halle, Germany
| | - Arie Geerlof
- Institute of Structural Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Brigitte Biesinger
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, 91054, Erlangen, Germany
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Johannes Kirchmair
- Universität Hamburg, Department of Informatics, Center for Bioinformatics (ZBH), 20146, Hamburg, Germany
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, 1090, Vienna, Austria
| | - Arnd Kieser
- Research Unit Signaling and Translation, Helmholtz Center Munich - German Research Center for Environmental Health, 85764, Neuherberg, Germany.
- Research Unit Gene Vectors, Helmholtz Center Munich - German Research Center for Environmental Health, 81377, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
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7
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Garrett SR, Mietrach N, Deme J, Bitzer A, Yang Y, Ulhuq FR, Kretschmer D, Heilbronner S, Smith TK, Lea SM, Palmer T. A type VII-secreted lipase toxin with reverse domain arrangement. Nat Commun 2023; 14:8438. [PMID: 38114483 PMCID: PMC10730906 DOI: 10.1038/s41467-023-44221-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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
The type VII protein secretion system (T7SS) is found in many Gram-positive bacteria and in pathogenic mycobacteria. All T7SS substrate proteins described to date share a common helical domain architecture at the N-terminus that typically interacts with other helical partner proteins, forming a composite signal sequence for targeting to the T7SS. The C-terminal domains are functionally diverse and in Gram-positive bacteria such as Staphylococcus aureus often specify toxic anti-bacterial activity. Here we describe the first example of a class of T7 substrate, TslA, that has a reverse domain organisation. TslA is widely found across Bacillota including Staphylococcus, Enterococcus and Listeria. We show that the S. aureus TslA N-terminal domain is a phospholipase A with anti-staphylococcal activity that is neutralised by the immunity lipoprotein TilA. Two small helical partner proteins, TlaA1 and TlaA2 are essential for T7-dependent secretion of TslA and at least one of these interacts with the TslA C-terminal domain to form a helical stack. Cryo-EM analysis of purified TslA complexes indicate that they share structural similarity with canonical T7 substrates. Our findings suggest that the T7SS has the capacity to recognise a secretion signal present at either end of a substrate.
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Affiliation(s)
- Stephen R Garrett
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Nicole Mietrach
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Justin Deme
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA
| | - Alina Bitzer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076, Tübingen, Germany
| | - Yaping Yang
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Fatima R Ulhuq
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Dorothee Kretschmer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076, Tübingen, Germany
| | - Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Terry K Smith
- School of Biology, Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, United Kingdom
| | - Susan M Lea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA
| | - Tracy Palmer
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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8
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Kreer C, Lupo C, Ercanoglu MS, Gieselmann L, Spisak N, Grossbach J, Schlotz M, Schommers P, Gruell H, Dold L, Beyer A, Nourmohammad A, Mora T, Walczak AM, Klein F. Probabilities of developing HIV-1 bNAb sequence features in uninfected and chronically infected individuals. Nat Commun 2023; 14:7137. [PMID: 37932288 PMCID: PMC10628170 DOI: 10.1038/s41467-023-42906-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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 10/24/2023] [Indexed: 11/08/2023] Open
Abstract
HIV-1 broadly neutralizing antibodies (bNAbs) are able to suppress viremia and prevent infection. Their induction by vaccination is therefore a major goal. However, in contrast to antibodies that neutralize other pathogens, HIV-1-specific bNAbs frequently carry uncommon molecular characteristics that might prevent their induction. Here, we perform unbiased sequence analyses of B cell receptor repertoires from 57 uninfected and 46 chronically HIV-1- or HCV-infected individuals and learn probabilistic models to predict the likelihood of bNAb development. We formally show that lower probabilities for bNAbs are predictive of higher HIV-1 neutralization activity. Moreover, ranking bNAbs by their probabilities allows to identify highly potent antibodies with superior generation probabilities as preferential targets for vaccination approaches. Importantly, we find equal bNAb probabilities across infected and uninfected individuals. This implies that chronic infection is not a prerequisite for the generation of bNAbs, fostering the hope that HIV-1 vaccines can induce bNAb development in uninfected people.
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Affiliation(s)
- Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Cosimo Lupo
- Laboratoire de physique de l'Ecole normale supérieure, CNRS, PSL University, Sorbonne Université, and Université Paris Cité, 75005, Paris, France
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma I, 00185, Rome, Italy
| | - Meryem S Ercanoglu
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Lutz Gieselmann
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- German Center for Infection Research, Partner Site Bonn-Cologne, 50931, Cologne, Germany
| | - Natanael Spisak
- Laboratoire de physique de l'Ecole normale supérieure, CNRS, PSL University, Sorbonne Université, and Université Paris Cité, 75005, Paris, France
| | - Jan Grossbach
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases & Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, 50931, Cologne, Germany
| | - Maike Schlotz
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Philipp Schommers
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- German Center for Infection Research, Partner Site Bonn-Cologne, 50931, Cologne, Germany
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931, Cologne, Germany
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
| | - Leona Dold
- Department of Internal Medicine I, University Hospital of Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
| | - Andreas Beyer
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases & Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931, Cologne, Germany
| | - Armita Nourmohammad
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077, Göttingen, Germany
- Department of Physics, University of Washington, 3910 15th Ave Northeast, Seattle, WA, 98195, USA
- Department of Applied Mathematics, University of Washington, 4182 W Stevens Way NE, Seattle, WA, 98105, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, 85 E Stevens Way NE, Seattle, WA, 98195, USA
- Fred Hutchinson Cancer Center, 1241 Eastlake Ave E, Seattle, WA, 98102, USA
| | - Thierry Mora
- Laboratoire de physique de l'Ecole normale supérieure, CNRS, PSL University, Sorbonne Université, and Université Paris Cité, 75005, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de physique de l'Ecole normale supérieure, CNRS, PSL University, Sorbonne Université, and Université Paris Cité, 75005, Paris, France
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
- German Center for Infection Research, Partner Site Bonn-Cologne, 50931, Cologne, Germany.
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931, Cologne, Germany.
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9
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Schommers P, Kim DS, Schlotz M, Kreer C, Eggeling R, Hake A, Stecher M, Park J, Radford CE, Dingens AS, Ercanoglu MS, Gruell H, Odidika S, Dahlhaus M, Gieselmann L, Ahmadov E, Lawong RY, Heger E, Knops E, Wyen C, Kümmerle T, Römer K, Scholten S, Wolf T, Stephan C, Suárez I, Raju N, Adhikari A, Esser S, Streeck H, Duerr R, Nanfack AJ, Zolla-Pazner S, Geldmacher C, Geisenberger O, Kroidl A, William W, Maganga L, Ntinginya NE, Georgiev IS, Vehreschild JJ, Hoelscher M, Fätkenheuer G, Lavinder JJ, Bloom JD, Seaman MS, Lehmann C, Pfeifer N, Georgiou G, Klein F. Dynamics and durability of HIV-1 neutralization are determined by viral replication. Nat Med 2023; 29:2763-2774. [PMID: 37957379 PMCID: PMC10667105 DOI: 10.1038/s41591-023-02582-3] [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: 02/26/2023] [Accepted: 09/07/2023] [Indexed: 11/15/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1)-neutralizing antibodies (nAbs) that prevent infection are the main goal of HIV vaccine discovery. But as no nAb-eliciting vaccines are yet available, only data from HIV-1 neutralizers-persons with HIV-1 who naturally develop broad and potent nAbs-can inform about the dynamics and durability of nAb responses in humans, knowledge which is crucial for the design of future HIV-1 vaccine regimens. To address this, we assessed HIV-1-neutralizing immunoglobulin G (IgG) from 2,354 persons with HIV-1 on or off antiretroviral therapy (ART). Infection with non-clade B viruses, CD4+ T cell counts <200 µl-1, being off ART and a longer time off ART were independent predictors of a more potent and broad neutralization. In longitudinal analyses, we found nAb half-lives of 9.3 and 16.9 years in individuals with no- or low-level viremia, respectively, and 4.0 years in persons who newly initiated ART. Finally, in a potent HIV-1 neutralizer, we identified lower fractions of serum nAbs and of nAb-encoding memory B cells after ART initiation, suggesting that a decreasing neutralizing serum activity after antigen withdrawal is due to lower levels of nAbs. These results collectively show that HIV-1-neutralizing responses can persist for several years, even at low antigen levels, suggesting that an HIV-1 vaccine may elicit a durable nAb response.
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Affiliation(s)
- Philipp Schommers
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Dae Sung Kim
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Maike Schlotz
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Christoph Kreer
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Ralf Eggeling
- Methods in Medical Informatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
| | - Anna Hake
- Research Group Computational Biology, Max Planck Institute for Informatics, Saarbrücken, Germany
- Saarland Informatics Campus, Saarbrücken, Germany
| | - Melanie Stecher
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Juyeon Park
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Caelan E Radford
- Molecular and Cellular Biology Graduate Program, University of Washington, and Basic Sciences Division, Fred Hutch Cancer Center, Seattle, WA, USA
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Adam S Dingens
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Meryem S Ercanoglu
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Henning Gruell
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Stanley Odidika
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Marten Dahlhaus
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Lutz Gieselmann
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Elvin Ahmadov
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Rene Y Lawong
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Eva Heger
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Elena Knops
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Christoph Wyen
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Praxis am Ebertplatz, Cologne, Germany
| | | | - Katja Römer
- Gemeinschaftspraxis Gotenring, Cologne, Germany
| | | | - Timo Wolf
- Infectious Diseases Division, Goethe University Frankfurt, University Hospital, Frankfurt am Main, Germany
| | - Christoph Stephan
- Infectious Diseases Division, Goethe University Frankfurt, University Hospital, Frankfurt am Main, Germany
| | - Isabelle Suárez
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Nagarajan Raju
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anurag Adhikari
- Department of Infection and Immunology, Kathmandu Research Institute for Biological Sciences, Lalitpur, Nepal
| | - Stefan Esser
- Department of Dermatology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Hendrik Streeck
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
- Institute of Virology, Medical Faculty, University Bonn, Bonn, Germany
| | - Ralf Duerr
- Department of Microbiology, New York University School of Medicine, New York City, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, New York City, NY, USA
- Vaccine Center, NYU Grossman School of Medicine, New York City, NY, USA
| | - Aubin J Nanfack
- Medical Diagnostic Center, Yaoundé, Cameroon
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Susan Zolla-Pazner
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Microbiology, Icahn School of Medicine, New York City, NY, USA
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, Munich, Germany
| | - Otto Geisenberger
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Arne Kroidl
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Wiston William
- Mbeya Medical Research Centre, National Institute for Medical Research, Mbeya, Tanzania
| | - Lucas Maganga
- Mbeya Medical Research Centre, National Institute for Medical Research, Mbeya, Tanzania
| | | | - Ivelin S Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Jörg J Vehreschild
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, Munich, Germany
- Unit Global Health, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Neuherberg, Germany
| | - Gerd Fätkenheuer
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Jason J Lavinder
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Clara Lehmann
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Nico Pfeifer
- Methods in Medical Informatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
| | - George Georgiou
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Florian Klein
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany.
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany.
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10
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Gündüz HA, Binder M, To XY, Mreches R, Bischl B, McHardy AC, Münch PC, Rezaei M. A self-supervised deep learning method for data-efficient training in genomics. Commun Biol 2023; 6:928. [PMID: 37696966 PMCID: PMC10495322 DOI: 10.1038/s42003-023-05310-2] [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: 02/08/2023] [Accepted: 09/01/2023] [Indexed: 09/13/2023] Open
Abstract
Deep learning in bioinformatics is often limited to problems where extensive amounts of labeled data are available for supervised classification. By exploiting unlabeled data, self-supervised learning techniques can improve the performance of machine learning models in the presence of limited labeled data. Although many self-supervised learning methods have been suggested before, they have failed to exploit the unique characteristics of genomic data. Therefore, we introduce Self-GenomeNet, a self-supervised learning technique that is custom-tailored for genomic data. Self-GenomeNet leverages reverse-complement sequences and effectively learns short- and long-term dependencies by predicting targets of different lengths. Self-GenomeNet performs better than other self-supervised methods in data-scarce genomic tasks and outperforms standard supervised training with ~10 times fewer labeled training data. Furthermore, the learned representations generalize well to new datasets and tasks. These findings suggest that Self-GenomeNet is well suited for large-scale, unlabeled genomic datasets and could substantially improve the performance of genomic models.
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Affiliation(s)
- Hüseyin Anil Gündüz
- Department of Statistics, LMU Munich, Munich, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - Martin Binder
- Department of Statistics, LMU Munich, Munich, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - Xiao-Yin To
- Department of Statistics, LMU Munich, Munich, Germany
- Munich Center for Machine Learning, Munich, Germany
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - René Mreches
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Bernd Bischl
- Department of Statistics, LMU Munich, Munich, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - Alice C McHardy
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Philipp C Münch
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124, Braunschweig, Germany.
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.
- German Center for Infection Research (DZIF), partner site Hannover Braunschweig, Braunschweig, Germany.
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
| | - Mina Rezaei
- Department of Statistics, LMU Munich, Munich, Germany.
- Munich Center for Machine Learning, Munich, Germany.
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11
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Weiss AS, Niedermeier LS, von Strempel A, Burrichter AG, Ring D, Meng C, Kleigrewe K, Lincetto C, Hübner J, Stecher B. Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community. Nat Commun 2023; 14:4780. [PMID: 37553336 PMCID: PMC10409746 DOI: 10.1038/s41467-023-40372-0] [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: 12/13/2022] [Accepted: 07/24/2023] [Indexed: 08/10/2023] Open
Abstract
A challenging task to understand health and disease-related microbiome signatures is to move beyond descriptive community-level profiling towards disentangling microbial interaction networks. Using a synthetic gut bacterial community, we aimed to study the role of individual members in community assembly, identify putative keystone species and test their influence across different environments. Single-species dropout experiments reveal that bacterial strain relationships strongly vary not only in different regions of the murine gut, but also across several standard culture media. Mechanisms involved in environment-dependent keystone functions in vitro include exclusive access to polysaccharides as well as bacteriocin production. Further, Bacteroides caecimuris and Blautia coccoides are found to play keystone roles in gnotobiotic mice by impacting community composition, the metabolic landscape and inflammatory responses. In summary, the presented study highlights the strong interdependency between bacterial community ecology and the biotic and abiotic environment. These results question the concept of universally valid keystone species in the gastrointestinal ecosystem and underline the context-dependency of both, keystone functions and bacterial interaction networks.
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Affiliation(s)
- Anna S Weiss
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Lisa S Niedermeier
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Alexandra von Strempel
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Anna G Burrichter
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Diana Ring
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Chiara Lincetto
- Division of Paediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Johannes Hübner
- Division of Paediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany.
- German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany.
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12
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Nehlmeier I, Kempf A, Arora P, Cossmann A, Dopfer-Jablonka A, Stankov MV, Schulz SR, Jäck HM, Behrens GMN, Pöhlmann S, Hoffmann M. Host cell entry and neutralisation sensitivity of the SARS-CoV-2 XBB.1.16 lineage. Cell Mol Immunol 2023; 20:969-971. [PMID: 37156807 PMCID: PMC10165563 DOI: 10.1038/s41423-023-01030-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/10/2023] Open
Affiliation(s)
- Inga Nehlmeier
- Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany
| | - Prerna Arora
- Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany
| | - Anne Cossmann
- Department of Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Alexandra Dopfer-Jablonka
- Department of Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Metodi V Stankov
- Department of Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Sebastian R Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Glückstraße 6, 91054, Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Glückstraße 6, 91054, Erlangen, Germany
| | - Georg M N Behrens
- Department of Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
- Centre for Individualized Infection Medicine (CiiM), Feodor-Lynen-Straße 7, 30625, Hannover, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany.
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany.
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany.
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany.
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13
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Hoffmann M, Arora P, Nehlmeier I, Kempf A, Cossmann A, Schulz SR, Morillas Ramos G, Manthey LA, Jäck HM, Behrens GMN, Pöhlmann S. Profound neutralization evasion and augmented host cell entry are hallmarks of the fast-spreading SARS-CoV-2 lineage XBB.1.5. Cell Mol Immunol 2023; 20:419-422. [PMID: 36869193 PMCID: PMC9982771 DOI: 10.1038/s41423-023-00988-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 02/18/2023] [Indexed: 03/05/2023] Open
Affiliation(s)
- Markus Hoffmann
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany.
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany.
| | - Prerna Arora
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany
| | - Anne Cossmann
- Department for Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Sebastian R Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Glückstraße 6, 91054, Erlangen, Germany
| | - Gema Morillas Ramos
- Department for Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Luis A Manthey
- Department for Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Glückstraße 6, 91054, Erlangen, Germany
| | - Georg M N Behrens
- Department for Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
- Centre for Individualized Infection Medicine (CiiM), Feodor-Lynen-Straße 7, 30625, Hannover, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany
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14
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Hörner C, Fiedler AH, Bodmer BS, Walz L, Scheuplein VA, Hutzler S, Matrosovich MN, von Messling V, Mühlebach MD. A protective measles virus-derived vaccine inducing long-lasting immune responses against influenza A virus H7N9. NPJ Vaccines 2023; 8:46. [PMID: 36964176 PMCID: PMC10037405 DOI: 10.1038/s41541-023-00643-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/09/2023] [Indexed: 03/26/2023] Open
Abstract
A novel Influenza A virus (subtype H7N9) emerged in spring 2013 and caused considerable mortality in zoonotically infected patients. To be prepared for potential pandemics, broadly effective and safe vaccines are crucial. Recombinant measles virus (MeV) encoding antigens of foreign pathogens constitutes a promising vector platform to generate novel vaccines. To characterize the efficacy of H7N9 antigens in a prototypic vaccine platform technology, we generated MeVs encoding either neuraminidase (N9) or hemagglutinin (H7). Moraten vaccine strain-derived vaccine candidates were rescued; they replicated with efficiency comparable to that of the measles vaccine, robustly expressed H7 and N9, and were genetically stable over 10 passages. Immunization of MeV-susceptible mice triggered the production of antibodies against H7 and N9, including hemagglutination-inhibiting and neutralizing antibodies induced by MVvac2-H7(P) and neuraminidase-inhibiting antibodies by MVvac2-N9(P). Vaccinated mice also developed long-lasting H7- and N9-specific T cells. Both MVvac2-H7(P) and MVvac2-N9(P)-vaccinated mice were protected from lethal H7N9 challenge.
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Affiliation(s)
- Cindy Hörner
- Section 4/3: Product Testing of IVMPs, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225, Langen, Germany
- German Center for Infection Research, Gießen-Marburg-Langen, Germany
| | - Anna H Fiedler
- Section 4/3: Product Testing of IVMPs, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225, Langen, Germany
- German Center for Infection Research, Gießen-Marburg-Langen, Germany
| | - Bianca S Bodmer
- Section 4/3: Product Testing of IVMPs, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225, Langen, Germany
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, 17493, Greifswald-Insel Riems, Germany
| | - Lisa Walz
- Section 4/0: Research in Veterinary Medicine, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225, Langen, Germany
| | - Vivian A Scheuplein
- Section 4/3: Product Testing of IVMPs, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225, Langen, Germany
| | - Stefan Hutzler
- Section 4/3: Product Testing of IVMPs, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225, Langen, Germany
| | - Mikhail N Matrosovich
- German Center for Infection Research, Gießen-Marburg-Langen, Germany
- Institute of Virology, Philipps University, Marburg, Germany
| | - Veronika von Messling
- German Center for Infection Research, Gießen-Marburg-Langen, Germany
- Section 4/0: Research in Veterinary Medicine, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225, Langen, Germany
| | - Michael D Mühlebach
- Section 4/3: Product Testing of IVMPs, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225, Langen, Germany.
- German Center for Infection Research, Gießen-Marburg-Langen, Germany.
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15
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Jensen BEO, Knops E, Cords L, Lübke N, Salgado M, Busman-Sahay K, Estes JD, Huyveneers LEP, Perdomo-Celis F, Wittner M, Gálvez C, Mummert C, Passaes C, Eberhard JM, Münk C, Hauber I, Hauber J, Heger E, De Clercq J, Vandekerckhove L, Bergmann S, Dunay GA, Klein F, Häussinger D, Fischer JC, Nachtkamp K, Timm J, Kaiser R, Harrer T, Luedde T, Nijhuis M, Sáez-Cirión A, Schulze Zur Wiesch J, Wensing AMJ, Martinez-Picado J, Kobbe G. In-depth virological and immunological characterization of HIV-1 cure after CCR5Δ32/Δ32 allogeneic hematopoietic stem cell transplantation. Nat Med 2023; 29:583-587. [PMID: 36807684 PMCID: PMC10033413 DOI: 10.1038/s41591-023-02213-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/09/2023] [Indexed: 02/22/2023]
Abstract
Despite scientific evidence originating from two patients published to date that CCR5Δ32/Δ32 hematopoietic stem cell transplantation (HSCT) can cure human immunodeficiency virus type 1 (HIV-1), the knowledge of immunological and virological correlates of cure is limited. Here we characterize a case of long-term HIV-1 remission of a 53-year-old male who was carefully monitored for more than 9 years after allogeneic CCR5Δ32/Δ32 HSCT performed for acute myeloid leukemia. Despite sporadic traces of HIV-1 DNA detected by droplet digital PCR and in situ hybridization assays in peripheral T cell subsets and tissue-derived samples, repeated ex vivo quantitative and in vivo outgrowth assays in humanized mice did not reveal replication-competent virus. Low levels of immune activation and waning HIV-1-specific humoral and cellular immune responses indicated a lack of ongoing antigen production. Four years after analytical treatment interruption, the absence of a viral rebound and the lack of immunological correlates of HIV-1 antigen persistence are strong evidence for HIV-1 cure after CCR5Δ32/Δ32 HSCT.
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Affiliation(s)
- Björn-Erik Ole Jensen
- Department of Gastroenterology, Hepatology and Infectious Diseases, Düsseldorf University Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany.
| | - Elena Knops
- Institute of Virology, University and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Leon Cords
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nadine Lübke
- Institute of Virology, Düsseldorf University Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Maria Salgado
- IrsiCaixa AIDS Research Institute, Barcelona, Spain
- Center for Biomedical Research in Infectious Diseases (CIBERINFEC), Carlos III Health Institute, Madrid, Spain
- Germans Trias i Pujol Research Institute, Barcelona, Spain
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Laura E P Huyveneers
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Federico Perdomo-Celis
- Institut Pasteur, Paris Cité University, HIV Inflammation and Persistence, Paris, France
| | - Melanie Wittner
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | | | - Christiane Mummert
- Infectious Diseases and Immunodeficiency Section, Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
- Bavarian Nordic, Martinsried, Germany
| | - Caroline Passaes
- Institut Pasteur, Paris Cité University, HIV Inflammation and Persistence, Paris, France
| | - Johanna M Eberhard
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Helmholtz Center for Infection Research, Helmholtz Institute for One Health, Greifswald, Germany
| | - Carsten Münk
- Department of Gastroenterology, Hepatology and Infectious Diseases, Düsseldorf University Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | | | - Joachim Hauber
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
| | - Eva Heger
- Institute of Virology, University and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Jozefien De Clercq
- HIV Cure Research Center and Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center and Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent, Belgium
| | - Silke Bergmann
- Infectious Diseases and Immunodeficiency Section, Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Gábor A Dunay
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
- University Children's Research, UCR@Kinder-UKE, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Florian Klein
- Institute of Virology, University and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Dieter Häussinger
- Department of Gastroenterology, Hepatology and Infectious Diseases, Düsseldorf University Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Johannes C Fischer
- Institute for Transplant Diagnostics and Cell Therapeutics, Düsseldorf University Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Kathrin Nachtkamp
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, Düsseldorf University Hospital, Heinrich Heine University, Düsseldorf, Germany
| | - Joerg Timm
- Institute of Virology, Düsseldorf University Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Rolf Kaiser
- Institute of Virology, University and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Thomas Harrer
- Infectious Diseases and Immunodeficiency Section, Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Tom Luedde
- Department of Gastroenterology, Hepatology and Infectious Diseases, Düsseldorf University Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Monique Nijhuis
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Asier Sáez-Cirión
- Institut Pasteur, Paris Cité University, HIV Inflammation and Persistence, Paris, France
| | - Julian Schulze Zur Wiesch
- Infectious Diseases Unit, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.
| | - Annemarie M J Wensing
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
- Ezintsha, University of the Witwatersrand, Johannesburg, South Africa
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Barcelona, Spain
- Center for Biomedical Research in Infectious Diseases (CIBERINFEC), Carlos III Health Institute, Madrid, Spain
- University of Vic-Central University of Catalonia, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Guido Kobbe
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, Düsseldorf University Hospital, Heinrich Heine University, Düsseldorf, Germany
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16
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Wanner N, Andrieux G, Badia-I-Mompel P, Edler C, Pfefferle S, Lindenmeyer MT, Schmidt-Lauber C, Czogalla J, Wong MN, Okabayashi Y, Braun F, Lütgehetmann M, Meister E, Lu S, Noriega MLM, Günther T, Grundhoff A, Fischer N, Bräuninger H, Lindner D, Westermann D, Haas F, Roedl K, Kluge S, Addo MM, Huber S, Lohse AW, Reiser J, Ondruschka B, Sperhake JP, Saez-Rodriguez J, Boerries M, Hayek SS, Aepfelbacher M, Scaturro P, Puelles VG, Huber TB. Molecular consequences of SARS-CoV-2 liver tropism. Nat Metab 2022; 4:310-319. [PMID: 35347318 PMCID: PMC8964418 DOI: 10.1038/s42255-022-00552-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/14/2022] [Indexed: 02/07/2023]
Abstract
Extrapulmonary manifestations of COVID-19 have gained attention due to their links to clinical outcomes and their potential long-term sequelae1. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) displays tropism towards several organs, including the heart and kidney. Whether it also directly affects the liver has been debated2,3. Here we provide clinical, histopathological, molecular and bioinformatic evidence for the hepatic tropism of SARS-CoV-2. We find that liver injury, indicated by a high frequency of abnormal liver function tests, is a common clinical feature of COVID-19 in two independent cohorts of patients with COVID-19 requiring hospitalization. Using autopsy samples obtained from a third patient cohort, we provide multiple levels of evidence for SARS-CoV-2 liver tropism, including viral RNA detection in 69% of autopsy liver specimens, and successful isolation of infectious SARS-CoV-2 from liver tissue postmortem. Furthermore, we identify transcription-, proteomic- and transcription factor-based activity profiles in hepatic autopsy samples, revealing similarities to the signatures associated with multiple other viral infections of the human liver. Together, we provide a comprehensive multimodal analysis of SARS-CoV-2 liver tropism, which increases our understanding of the molecular consequences of severe COVID-19 and could be useful for the identification of organ-specific pharmacological targets.
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Affiliation(s)
- Nicola Wanner
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Pau Badia-I-Mompel
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, BioQuant, Heidelberg, Germany
| | - Carolin Edler
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Susanne Pfefferle
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maja T Lindenmeyer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Jan Czogalla
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Milagros N Wong
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yusuke Okabayashi
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fabian Braun
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marc Lütgehetmann
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Elisabeth Meister
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Shun Lu
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maria L M Noriega
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Günther
- Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Adam Grundhoff
- Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Nicole Fischer
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hanna Bräuninger
- Department of Cardiology, University Heart and Vascular Centre Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Diana Lindner
- Department of Cardiology, University Heart and Vascular Centre Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Dirk Westermann
- Department of Cardiology, University Heart and Vascular Centre Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Fabian Haas
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kevin Roedl
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Kluge
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marylyn M Addo
- I. Department of Medicine, University Medical Hospital Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Samuel Huber
- I. Department of Medicine, University Medical Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Ansgar W Lohse
- I. Department of Medicine, University Medical Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Jochen Reiser
- Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Benjamin Ondruschka
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jan P Sperhake
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, BioQuant, Heidelberg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium and German Cancer Research Center, Partner Site Freiburg, Freiburg, Germany
| | - Salim S Hayek
- Division of Cardiology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Pietro Scaturro
- Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Victor G Puelles
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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17
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Meng N, Grimm D. Membrane-destabilizing ionizable phospholipids: Novel components for organ-selective mRNA delivery and CRISPR-Cas gene editing. Signal Transduct Target Ther 2021; 6:206. [PMID: 34035211 PMCID: PMC8149719 DOI: 10.1038/s41392-021-00642-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/16/2021] [Accepted: 04/29/2021] [Indexed: 12/15/2022] Open
Affiliation(s)
- Ning Meng
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, Heidelberg, Germany.
- BioQuant, University of Heidelberg, Heidelberg, Germany.
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, Heidelberg, Germany.
- BioQuant, University of Heidelberg, Heidelberg, Germany.
- German Center for Infection Research (DZIF) and German Center for Cardiovascular Research (DZHK), partner site Heidelberg, Heidelberg, Germany.
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Zapatka M, Borozan I, Brewer DS, Iskar M, Grundhoff A, Alawi M, Desai N, Sültmann H, Moch H, Cooper CS, Eils R, Ferretti V, Lichter P. The landscape of viral associations in human cancers. Nat Genet 2020; 52:320-330. [PMID: 32025001 PMCID: PMC8076016 DOI: 10.1038/s41588-019-0558-9] [Citation(s) in RCA: 216] [Impact Index Per Article: 54.0] [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: 11/30/2018] [Accepted: 11/22/2019] [Indexed: 12/30/2022]
Abstract
Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, for which whole-genome and-for a subset-whole-transcriptome sequencing data from 2,658 cancers across 38 tumor types was aggregated, we systematically investigated potential viral pathogens using a consensus approach that integrated three independent pipelines. Viruses were detected in 382 genome and 68 transcriptome datasets. We found a high prevalence of known tumor-associated viruses such as Epstein-Barr virus (EBV), hepatitis B virus (HBV) and human papilloma virus (HPV; for example, HPV16 or HPV18). The study revealed significant exclusivity of HPV and driver mutations in head-and-neck cancer and the association of HPV with APOBEC mutational signatures, which suggests that impaired antiviral defense is a driving force in cervical, bladder and head-and-neck carcinoma. For HBV, HPV16, HPV18 and adeno-associated virus-2 (AAV2), viral integration was associated with local variations in genomic copy numbers. Integrations at the TERT promoter were associated with high telomerase expression evidently activating this tumor-driving process. High levels of endogenous retrovirus (ERV1) expression were linked to a worse survival outcome in patients with kidney cancer.
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Affiliation(s)
- Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ivan Borozan
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Daniel S Brewer
- Norwich Medical School, University of East Anglia, Norwich, UK
- Earlham Institute, Norwich, UK
| | - Murat Iskar
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Adam Grundhoff
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Borstel-Lübeck-Riems, Hamburg, Germany
| | - Malik Alawi
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nikita Desai
- Bioinformatics Group, Department of Computer Science, University College London, London, UK
- Biomedical Data Science Laboratory, Francis Crick Institute, London, UK
| | - Holger Sültmann
- National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University and University Hospital Zürich, Zurich, Switzerland
| | - Colin S Cooper
- Norwich Medical School, University of East Anglia, Norwich, UK
- Earlham Institute, Norwich, UK
- Institute of Cancer Research, London, UK
- University of East Anglia, Norwich, UK
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University and BioQuant Center, Heidelberg, Germany
- Center for Digital Health, Berlin Institute of Health and Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Vincent Ferretti
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, Québec, Canada
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
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