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Schrempf M, Kirmair MA, Mair A, Hoffmann M, Dannecker C, Anthuber M, Anthuber L. Incidence and clinical features of endometriosis in 2484 consecutive female patients undergoing appendectomy for suspected appendicitis-a retrospective analysis. Langenbecks Arch Surg 2024; 409:144. [PMID: 38684518 PMCID: PMC11059005 DOI: 10.1007/s00423-024-03328-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/18/2024] [Indexed: 05/02/2024]
Abstract
INTRODUCTION Endometriosis is a common condition affecting 5 to 10% of women of childbearing age. The true incidence of endometriosis of the appendix is currently unknown. Since symptoms often overlap with those of acute appendicitis, endometriosis of the appendix presents a diagnostic challenge in the emergency department. This large retrospective study investigates the incidence and perioperative clinical, radiologic, and laboratory findings, as well as possible differences between patients with and without endometriosis. METHODS Data from consecutive patients who underwent appendectomy for suspected appendicitis without a history of endometriosis were analyzed. Perioperative clinical, laboratory, perioperative, and histopathologic findings were compared between women with and without endometriosis. RESULTS Between January 2008 and June 2023, 2484 consecutive patients without a history of endometriosis underwent urgent appendectomy for suspected appendicitis. Endometriosis was detected on histopathologic examination in 17 (0.7%) patients. Signs of appendicitis were found less frequently on ultrasound in the endometriosis group compared to the non-endometriosis group (23.4% vs. 61.5%; p = 0.002; OR = 0.193; 95% CI 0.063-0.593). There were no differences in physical examination findings, duration of symptoms, degree of inflammation, surgical outcomes, or complication rates. CONCLUSION The incidence of endometriosis of the appendix in patients undergoing appendectomy for suspected appendicitis was higher than suggested by data from autopsy series and populations with biopsy-proven endometriosis. Patients with endometriosis of the appendix were less likely to have a positive ultrasound finding, but perioperative and histopathologic findings and severity of inflammation did not differ from patients without endometriosis, presenting diagnostic challenges for clinicians.
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Affiliation(s)
- M Schrempf
- Department of General, Visceral and Transplantation Surgery, University Hospital Augsburg, Stenglinstrasse 2, 86156, Augsburg, Germany.
| | - M-A Kirmair
- Department of General, Visceral and Transplantation Surgery, University Hospital Augsburg, Stenglinstrasse 2, 86156, Augsburg, Germany
| | - A Mair
- Department of General, Visceral and Transplantation Surgery, University Hospital Augsburg, Stenglinstrasse 2, 86156, Augsburg, Germany
| | - M Hoffmann
- Department of General, Visceral and Transplantation Surgery, University Hospital Augsburg, Stenglinstrasse 2, 86156, Augsburg, Germany
| | - C Dannecker
- Department of Gynecology and Obstetrics, University Hospital Augsburg, University of Augsburg, Augsburg, Germany
| | - M Anthuber
- Department of General, Visceral and Transplantation Surgery, University Hospital Augsburg, Stenglinstrasse 2, 86156, Augsburg, Germany
| | - L Anthuber
- Department of General, Visceral and Transplantation Surgery, University Hospital Augsburg, Stenglinstrasse 2, 86156, Augsburg, Germany
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Jäger N, Ayyub SA, Peske F, Liedtke D, Bohne J, Hoffmann M, Rodnina MV, Pöhlmann S. The Inhibition of Gag-Pol Expression by the Restriction Factor Shiftless Is Dispensable for the Restriction of HIV-1 Infection. Viruses 2024; 16:583. [PMID: 38675925 PMCID: PMC11055011 DOI: 10.3390/v16040583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
The interferon-induced host cell protein Shiftless (SFL) inhibits -1 programmed ribosomal frameshifting (-1PRF) required for the expression of HIV-1 Gal-Pol and the formation of infectious HIV-1 particles. However, the specific regions in SFL required for antiviral activity and the mechanism by which SFL inhibits -1PRF remain unclear. Employing alanine scanning mutagenesis, we found that basic amino acids in the predicted zinc ribbon motif of SFL are essential for the suppression of Gag-Pol expression but dispensable for anti-HIV-1 activity. We have shown that SFL inhibits the expression of the murine leukemia virus (MLV) Gag-Pol polyprotein and the formation of infectious MLV particles, although Gag-Pol expression of MLV is independent of -1PRF but requires readthrough of a stop codon. These findings indicate that SFL might inhibit HIV-1 infection by more than one mechanism and that SFL might target programmed translational readthrough as well as -1PRF signals, both of which are regulated by mRNA secondary structure elements.
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Affiliation(s)
- Niklas Jäger
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, 37077 Göttingen, Germany;
- Faculty of Biology and Psychology, University Göttingen, 37073 Göttingen, Germany
| | - Shreya Ahana Ayyub
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; (S.A.A.); (F.P.); (D.L.); (M.V.R.)
| | - Frank Peske
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; (S.A.A.); (F.P.); (D.L.); (M.V.R.)
| | - David Liedtke
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; (S.A.A.); (F.P.); (D.L.); (M.V.R.)
| | - Jens Bohne
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany;
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, 37077 Göttingen, Germany;
- Faculty of Biology and Psychology, University Göttingen, 37073 Göttingen, Germany
| | - Marina V. Rodnina
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; (S.A.A.); (F.P.); (D.L.); (M.V.R.)
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, 37077 Göttingen, Germany;
- Faculty of Biology and Psychology, University Göttingen, 37073 Göttingen, Germany
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Bruhn M, Obara M, Salam A, Costa B, Ziegler A, Waltl I, Pavlou A, Hoffmann M, Graalmann T, Pöhlmann S, Schambach A, Kalinke U. Diversification of the VH3-53 immunoglobulin gene segment by somatic hypermutation results in neutralization of SARS-CoV-2 virus variants. Eur J Immunol 2024:e2451056. [PMID: 38593351 DOI: 10.1002/eji.202451056] [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: 02/07/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
COVID-19 induces re-circulating long-lived memory B cells (MBC) that, upon re-encounter with the pathogen, are induced to mount immunoglobulin responses. During convalescence, antibodies are subjected to affinity maturation, which enhances the antibody binding strength and generates new specificities that neutralize virus variants. Here, we performed a single-cell RNA sequencing analysis of spike-specific B cells from a SARS-CoV-2 convalescent subject. After COVID-19 vaccination, matured infection-induced MBC underwent recall and differentiated into plasmablasts. Furthermore, the transcriptomic profiles of newly activated B cells transiently shifted toward the ones of atypical and CXCR3+ B cells and several B-cell clonotypes massively expanded. We expressed monoclonal antibodies (mAbs) from all B-cell clones from the largest clonotype that used the VH3-53 gene segment. The in vitro analysis revealed that some somatic hypermutations enhanced the neutralization breadth of mAbs in a putatively stochastic manner. Thus, somatic hypermutation of B-cell clonotypes generates an anticipatory memory that can neutralize new virus variants.
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Affiliation(s)
- Matthias Bruhn
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Maureen Obara
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Abdus Salam
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Bibiana Costa
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Annett Ziegler
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Inken Waltl
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Andreas Pavlou
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology, Georg-August-University Göttingen, Göttingen, Germany
| | - Theresa Graalmann
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
- Junior Research Group for Translational Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
- Biomedical Research in End-Stage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology, Georg-August-University Göttingen, Göttingen, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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4
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Haro Mares NB, Döller SC, Wissel T, Hoffmann M, Vogel M, Buntkowsky G. Structures and Dynamics of Complex Guest Molecules in Confinement, Revealed by Solid-State NMR, Molecular Dynamics, and Calorimetry. Molecules 2024; 29:1669. [PMID: 38611950 PMCID: PMC11013127 DOI: 10.3390/molecules29071669] [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: 02/29/2024] [Revised: 03/29/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
This review gives an overview of current trends in the investigation of confined molecules such as water, small and higher alcohols, carbonic acids, ethylene glycol, and non-ionic surfactants, such as polyethylene glycol or Triton-X, as guest molecules in neat and functionalized mesoporous silica materials employing solid-state NMR spectroscopy, supported by calorimetry and molecular dynamics simulations. The combination of steric interactions, hydrogen bonds, and hydrophobic and hydrophilic interactions results in a fascinating phase behavior in the confinement. Combining solid-state NMR and relaxometry, DNP hyperpolarization, molecular dynamics simulations, and general physicochemical techniques, it is possible to monitor these confined molecules and gain deep insights into this phase behavior and the underlying molecular arrangements. In many cases, the competition between hydrogen bonding and electrostatic interactions between polar and non-polar moieties of the guests and the host leads to the formation of ordered structures, despite the cramped surroundings inside the pores.
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Affiliation(s)
- Nadia B. Haro Mares
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, D-64287 Darmstadt, Germany; (N.B.H.M.); (S.C.D.); (T.W.)
| | - Sonja C. Döller
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, D-64287 Darmstadt, Germany; (N.B.H.M.); (S.C.D.); (T.W.)
| | - Till Wissel
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, D-64287 Darmstadt, Germany; (N.B.H.M.); (S.C.D.); (T.W.)
| | - Markus Hoffmann
- Department of Chemistry and Biochemistry, State University of New York at Brockport, Brockport, NY 14420, USA
| | - Michael Vogel
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, D-64289 Darmstadt, Germany
| | - Gerd Buntkowsky
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, D-64287 Darmstadt, Germany; (N.B.H.M.); (S.C.D.); (T.W.)
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5
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Groß R, Reßin H, von Maltitz P, Albers D, Schneider L, Bley H, Hoffmann M, Cortese M, Gupta D, Deniz M, Choi JY, Jansen J, Preußer C, Seehafer K, Pöhlmann S, Voelker DR, Goffinet C, Pogge-von Strandmann E, Bunz U, Bartenschlager R, El Andaloussi S, Sparrer KMJ, Herker E, Becker S, Kirchhoff F, Münch J, Müller JA. Phosphatidylserine-exposing extracellular vesicles in body fluids are an innate defence against apoptotic mimicry viral pathogens. Nat Microbiol 2024; 9:905-921. [PMID: 38528146 PMCID: PMC10994849 DOI: 10.1038/s41564-024-01637-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 02/14/2024] [Indexed: 03/27/2024]
Abstract
Some viruses are rarely transmitted orally or sexually despite their presence in saliva, breast milk, or semen. We previously identified that extracellular vesicles (EVs) in semen and saliva inhibit Zika virus infection. However, the antiviral spectrum and underlying mechanism remained unclear. Here we applied lipidomics and flow cytometry to show that these EVs expose phosphatidylserine (PS). By blocking PS receptors, targeted by Zika virus in the process of apoptotic mimicry, they interfere with viral attachment and entry. Consequently, physiological concentrations of EVs applied in vitro efficiently inhibited infection by apoptotic mimicry dengue, West Nile, Chikungunya, Ebola and vesicular stomatitis viruses, but not severe acute respiratory syndrome coronavirus 2, human immunodeficiency virus 1, hepatitis C virus and herpesviruses that use other entry receptors. Our results identify the role of PS-rich EVs in body fluids in innate defence against infection via viral apoptotic mimicries, explaining why these viruses are primarily transmitted via PS-EV-deficient blood or blood-ingesting arthropods rather than direct human-to-human contact.
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Affiliation(s)
- Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Hanna Reßin
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Pascal von Maltitz
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Dan Albers
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Laura Schneider
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Hanna Bley
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Georg-August University Göttingen, Göttingen, Germany
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Dhanu Gupta
- Biomolecular Medicine, Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Miriam Deniz
- Clinic for Gynecology and Obstetrics, Ulm University Medical Center, Ulm, Germany
| | - Jae-Yeon Choi
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Jenny Jansen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Preußer
- Core Facility Extracellular Vesicles, Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University Marburg, Marburg, Germany
| | - Kai Seehafer
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität, Heidelberg, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Georg-August University Göttingen, Göttingen, Germany
| | | | - Christine Goffinet
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Elke Pogge-von Strandmann
- Core Facility Extracellular Vesicles, Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University Marburg, Marburg, Germany
| | - Uwe Bunz
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Samir El Andaloussi
- Biomolecular Medicine, Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Eva Herker
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Stephan Becker
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Janis A Müller
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany.
- Institute of Virology, Philipps University Marburg, Marburg, Germany.
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6
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Oliveira BR, Nehlmeier I, Kempf AM, Venugopalan V, Rehders M, Ceniza MEP, Cavalcanti PADTPV, Hoffmann M, Pöhlmann S, Brix K. Cytoskeletal β-tubulin and cysteine cathepsin L deregulation by SARS-CoV-2 spike protein interaction with the neuronal model cell line SH-SY5Y. Biochimie 2024:S0300-9084(24)00044-0. [PMID: 38432290 DOI: 10.1016/j.biochi.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024]
Abstract
SARS-CoV-2 mainly infects the respiratory tract but can also target other organs, including the central nervous system. While it was recently shown that cells of the blood-brain-barrier are permissive to SARS-CoV-2 infection in vitro, it remains debated whether neurons can be infected. In this study, we demonstrate that vesicular stomatitis virus particles pseudotyped with the spike protein of SARS-CoV-2 variants WT, Alpha, Delta and Omicron enter the neuronal model cell line SH-SY5Y. Cell biological analyses of the pseudo-virus treated cultures showed marked alterations in microtubules of SH-SY5Y cells. Because the changes in β-tubulin occurred in most cells, but only few were infected, we further asked whether interaction of the cells with spike protein might be sufficient to cause molecular and structural changes. For this, SH-SY5Y cells were incubated with trimeric spike proteins for time intervals of up to 24 h. CellProfiler™-based image analyses revealed changes in the intensities of microtubule staining in spike protein-incubated cells. Furthermore, expression of the spike protein-processing protease cathepsin L was found to be up-regulated by wild type, Alpha and Delta spike protein pseudotypes and cathepsin L was found to be secreted from spike protein-treated cells. We conclude that the mere interaction of the SARS-CoV-2 with neuronal cells can affect cellular architecture and proteolytic capacities. The molecular mechanisms underlying SARS-CoV-2 spike protein induced cytoskeletal changes in neuronal cells remain elusive and require future studies.
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Affiliation(s)
- Bernardo R Oliveira
- Constructor University, School of Science, Campus Ring 1, D-28759, Bremen, Germany
| | - Inga Nehlmeier
- Deutsches Primatenzentrum - Leibniz-Institut für Primatenforschung, Abteilung Infektionsbiologie, Kellnerweg 4, D-37077, Göttingen, Germany.
| | - Amy Madeleine Kempf
- Deutsches Primatenzentrum - Leibniz-Institut für Primatenforschung, Abteilung Infektionsbiologie, Kellnerweg 4, D-37077, Göttingen, Germany; Faculty of Biology and Psychology, Georg-August University Göttingen, Wilhelmsplatz 1, D-37073, Göttingen, Germany.
| | | | - Maren Rehders
- Constructor University, School of Science, Campus Ring 1, D-28759, Bremen, Germany.
| | - Marianne E P Ceniza
- Constructor University, School of Science, Campus Ring 1, D-28759, Bremen, Germany.
| | | | - Markus Hoffmann
- Deutsches Primatenzentrum - Leibniz-Institut für Primatenforschung, Abteilung Infektionsbiologie, Kellnerweg 4, D-37077, Göttingen, Germany; Faculty of Biology and Psychology, Georg-August University Göttingen, Wilhelmsplatz 1, D-37073, Göttingen, Germany.
| | - Stefan Pöhlmann
- Deutsches Primatenzentrum - Leibniz-Institut für Primatenforschung, Abteilung Infektionsbiologie, Kellnerweg 4, D-37077, Göttingen, Germany; Faculty of Biology and Psychology, Georg-August University Göttingen, Wilhelmsplatz 1, D-37073, Göttingen, Germany.
| | - Klaudia Brix
- Constructor University, School of Science, Campus Ring 1, D-28759, Bremen, Germany.
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7
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Cossmann A, Hoffmann M, Stankov MV, Lürken K, Morillas Ramos G, Kempf A, Nehlmeier I, Pöhlmann S, Behrens GMN, Dopfer-Jablonka A. Immune responses following BNT162b2 XBB.1.5 vaccination in patients on haemodialysis in Germany. Lancet Infect Dis 2024; 24:e145-e146. [PMID: 38211602 DOI: 10.1016/s1473-3099(23)00783-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/13/2024]
Affiliation(s)
- Anne Cossmann
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Markus Hoffmann
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Metodi V Stankov
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | | | - Gema Morillas Ramos
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center, Leibniz-Institute for Primate Research, Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center, Leibniz-Institute for Primate Research, Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Leibniz-Institute for Primate Research, Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Georg M N Behrens
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany; CiiM, Center for Individualised Infection Medicine, Hannover, Germany.
| | - Alexandra Dopfer-Jablonka
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
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8
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Chiyyeadu A, Asgedom G, Bruhn M, Rocha C, Schlegel TU, Neumann T, Galla M, Vollmer Barbosa P, Hoffmann M, Ehrhardt K, Ha TC, Morgan M, Schoeder CT, Pöhlmann S, Kalinke U, Schambach A. A tetravalent bispecific antibody outperforms the combination of its parental antibodies and neutralizes diverse SARS-CoV-2 variants. Clin Immunol 2024; 260:109902. [PMID: 38218210 DOI: 10.1016/j.clim.2024.109902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
The devastating impact of COVID-19 on global health shows the need to increase our pandemic preparedness. Recombinant therapeutic antibodies were successfully used to treat and protect at-risk patients from COVID-19. However, the currently circulating Omicron subvariants of SARS-CoV-2 are largely resistant to therapeutic antibodies, and novel approaches to generate broadly neutralizing antibodies are urgently needed. Here, we describe a tetravalent bispecific antibody, A7A9 TVB, which actively neutralized many SARS-CoV-2 variants of concern, including early Omicron subvariants. Interestingly, A7A9 TVB neutralized more variants at lower concentration as compared to the combination of its parental monoclonal antibodies, A7K and A9L. A7A9 also reduced the viral load of authentic Omicron BA.1 virus in infected pseudostratified primary human nasal epithelial cells. Overall, A7A9 displayed the characteristics of a potent broadly neutralizing antibody, which may be suitable for prophylactic and therapeutic applications in the clinics, thus highlighting the usefulness of an effective antibody-designing approach.
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Affiliation(s)
- Abhishek Chiyyeadu
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Girmay Asgedom
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Matthias Bruhn
- Institute for Experimental Infection Research, TWINCORE, Center for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625 Hannover, Germany
| | - Cheila Rocha
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Tom U Schlegel
- Institute for Drug Discovery, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Thomas Neumann
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Melanie Galla
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Philippe Vollmer Barbosa
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Markus Hoffmann
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Katrin Ehrhardt
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Teng-Cheong Ha
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Michael Morgan
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Clara T Schoeder
- Institute for Drug Discovery, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Stefan Pöhlmann
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Center for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625 Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, United States of America.
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9
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Metzdorf K, Jacobsen H, Kim Y, Teixeira Alves LG, Kulkarni U, Eschke K, Chaudhry MZ, Hoffmann M, Bertoglio F, Ruschig M, Hust M, Cokarić Brdovčak M, Materljan J, Šustić M, Krmpotić A, Jonjić S, Widera M, Ciesek S, Pöhlmann S, Landthaler M, Čičin-Šain L. A single-dose MCMV-based vaccine elicits long-lasting immune protection in mice against distinct SARS-CoV-2 variants. bioRxiv 2024:2022.11.25.517953. [PMID: 36482969 PMCID: PMC9727759 DOI: 10.1101/2022.11.25.517953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Current vaccines against COVID-19 elicit immune responses that are overall strong but wane rapidly. As a consequence, the necessary booster shots have led to vaccine fatigue. Hence, vaccines that would provide lasting protection against COVID-19 are needed, but are still unavailable. Cytomegaloviruses (CMV) elicit lasting and uniquely strong immune responses. Used as vaccine vectors, they may be attractive tools that obviate the need for boosters. Therefore, we tested the murine CMV (MCMV) as a vaccine vector against COVID-19 in relevant preclinical models of immunization and challenge. We have previously developed a recombinant murine CMV (MCMV) vaccine vector expressing the spike protein of the ancestral SARS-CoV-2 (MCMVS). In this study, we show that the MCMVS elicits a robust and lasting protection in young and aged mice. Notably, S-specific humoral and cellular immunity was not only maintained but even increased over a period of at least 6 months. During that time, antibody avidity continuously increased and expanded in breadth, resulting in neutralization of genetically distant variants, like Omicron BA.1. A single dose of MCMVS conferred rapid virus clearance upon challenge. Moreover, MCMVS vaccination controlled two immune-evading variants of concern (VoCs), the Beta (B.1.135) and the Omicron (BA.1) variants. Thus, CMV vectors provide unique advantages over other vaccine technologies, eliciting broadly reactive and long-lasting immune responses against COVID-19.
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Affiliation(s)
- Kristin Metzdorf
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Henning Jacobsen
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Yeonsu Kim
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Luiz Gustavo Teixeira Alves
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Upasana Kulkarni
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Kathrin Eschke
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - M. Zeeshan Chaudhry
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center – Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Federico Bertoglio
- Department of Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Maximilian Ruschig
- Department of Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Hust
- Department of Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Jelena Materljan
- Center for Proteomics, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
- Department of Histology and Embryology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Marko Šustić
- Center for Proteomics, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Astrid Krmpotić
- Department of Histology and Embryology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Stipan Jonjić
- Center for Proteomics, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt am Main, Germany
- German Centre for Infection Research (DZIF), External partner site Frankfurt, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center – Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Luka Čičin-Šain
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Centre for Individualized Infection Medicine (CiiM), a joint venture of HZI and MHH, Hannover, Germany
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10
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Hoffmann M, Willruth LL, Dietrich A, Lee HK, Knabl L, Trummer N, Baumbach J, Furth PA, Hennighausen L, List M. Blood transcriptomics analysis offers insights into variant-specific immune response to SARS-CoV-2. Sci Rep 2024; 14:2808. [PMID: 38307916 PMCID: PMC10837437 DOI: 10.1038/s41598-024-53117-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: 11/03/2023] [Accepted: 01/28/2024] [Indexed: 02/04/2024] Open
Abstract
Bulk RNA sequencing (RNA-seq) of blood is typically used for gene expression analysis in biomedical research but is still rarely used in clinical practice. In this study, we propose that RNA-seq should be considered a diagnostic tool, as it offers not only insights into aberrant gene expression and splicing but also delivers additional readouts on immune cell type composition as well as B-cell and T-cell receptor (BCR/TCR) repertoires. We demonstrate that RNA-seq offers insights into a patient's immune status via integrative analysis of RNA-seq data from patients infected with various SARS-CoV-2 variants (in total 196 samples with up to 200 million reads sequencing depth). We compare the results of computational cell-type deconvolution methods (e.g., MCP-counter, xCell, EPIC, quanTIseq) to complete blood count data, the current gold standard in clinical practice. We observe varying levels of lymphocyte depletion and significant differences in neutrophil levels between SARS-CoV-2 variants. Additionally, we identify B and T cell receptor (BCR/TCR) sequences using the tools MiXCR and TRUST4 to show that-combined with sequence alignments and BLASTp-they could be used to classify a patient's disease. Finally, we investigated the sequencing depth required for such analyses and concluded that 10 million reads per sample is sufficient. In conclusion, our study reveals that computational cell-type deconvolution and BCR/TCR methods using bulk RNA-seq analyses can supplement missing CBC data and offer insights into immune responses, disease severity, and pathogen-specific immunity, all achievable with a sequencing depth of 10 million reads per sample.
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Affiliation(s)
- Markus Hoffmann
- Data Science in Systems Biomedicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
- Institute for Advanced Study, Technical University of Munich, Lichtenbergstrasse 2 a, 85748, Garching, Germany.
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD, 20892, USA.
| | - Lina-Liv Willruth
- Data Science in Systems Biomedicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Alexander Dietrich
- Data Science in Systems Biomedicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Hye Kyung Lee
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD, 20892, USA
| | | | - Nico Trummer
- Data Science in Systems Biomedicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Jan Baumbach
- Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Computational BioMedicine Lab, University of Southern Denmark, Odense, Denmark
| | - Priscilla A Furth
- Institute for Advanced Study, Technical University of Munich, Lichtenbergstrasse 2 a, 85748, Garching, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD, 20892, USA
- Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA
| | - Lothar Hennighausen
- Institute for Advanced Study, Technical University of Munich, Lichtenbergstrasse 2 a, 85748, Garching, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD, 20892, USA
| | - Markus List
- Data Science in Systems Biomedicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
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11
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Zhang L, Kempf A, Nehlmeier I, Cossmann A, Richter A, Bdeir N, Graichen L, Moldenhauer AS, Dopfer-Jablonka A, Stankov MV, Simon-Loriere E, Schulz SR, Jäck HM, Čičin-Šain L, Behrens GMN, Drosten C, Hoffmann M, Pöhlmann S. SARS-CoV-2 BA.2.86 enters lung cells and evades neutralizing antibodies with high efficiency. Cell 2024; 187:596-608.e17. [PMID: 38194966 DOI: 10.1016/j.cell.2023.12.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/03/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024]
Abstract
BA.2.86, a recently identified descendant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2 sublineage, contains ∼35 mutations in the spike (S) protein and spreads in multiple countries. Here, we investigated whether the virus exhibits altered biological traits, focusing on S protein-driven viral entry. Employing pseudotyped particles, we show that BA.2.86, unlike other Omicron sublineages, enters Calu-3 lung cells with high efficiency and in a serine- but not cysteine-protease-dependent manner. Robust lung cell infection was confirmed with authentic BA.2.86, but the virus exhibited low specific infectivity. Further, BA.2.86 was highly resistant against all therapeutic antibodies tested, efficiently evading neutralization by antibodies induced by non-adapted vaccines. In contrast, BA.2.86 and the currently circulating EG.5.1 sublineage were appreciably neutralized by antibodies induced by the XBB.1.5-adapted vaccine. Collectively, BA.2.86 has regained a trait characteristic of early SARS-CoV-2 lineages, robust lung cell entry, and evades neutralizing antibodies. However, BA.2.86 exhibits low specific infectivity, which might limit transmissibility.
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Affiliation(s)
- Lu Zhang
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany
| | - Anne Cossmann
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Anja Richter
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Najat Bdeir
- Department of Viral Immunology, Helmholtz Zentrum für Infektionsforschung, 38124 Braunschweig, Germany
| | - Luise Graichen
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | | | - Alexandra Dopfer-Jablonka
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany
| | - Metodi V Stankov
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Etienne Simon-Loriere
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, 75015 Paris, France; National Reference Center for Viruses of respiratory Infections, Institut Pasteur, 75015 Paris, France
| | - Sebastian R Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Luka Čičin-Šain
- Department of Viral Immunology, Helmholtz Zentrum für Infektionsforschung, 38124 Braunschweig, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany; Center for Individualized Infection Medicine, a joint venture of HZI and MHH, 30625 Hannover, Germany
| | - Georg M N Behrens
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany; Center for Individualized Infection Medicine, a joint venture of HZI and MHH, 30625 Hannover, Germany
| | - Christian Drosten
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany.
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany.
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12
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Lio CT, Düz T, Hoffmann M, Willruth LL, Baumbach J, List M, Tsoy O. Comprehensive benchmark of differential transcript usage analysis for static and dynamic conditions. bioRxiv 2024:2024.01.14.575548. [PMID: 38313260 PMCID: PMC10836064 DOI: 10.1101/2024.01.14.575548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
RNA sequencing offers unique insights into transcriptome diversity, and a plethora of tools have been developed to analyze alternative splicing. One important task is to detect changes in the relative transcript abundance in differential transcript usage (DTU) analysis. The choice of the right analysis tool is non-trivial and depends on experimental factors such as the availability of single- or paired-end and bulk or single-cell data. To help users select the most promising tool for their task, we performed a comprehensive benchmark of DTU detection tools. We cover a wide array of experimental settings, using simulated bulk and single-cell RNA-seq data as well as real transcriptomics datasets, including time-series data. Our results suggest that DEXSeq, edgeR, and LimmaDS are better choices for paired-end data, while DSGseq and DEXSeq can be used for single-end data. In single-cell simulation settings, we showed that satuRn performs better than DTUrtle. In addition, we showed that Spycone is optimal for time series DTU/IS analysis based on the evidence provided using GO terms enrichment analysis.
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Affiliation(s)
- Chit Tong Lio
- Data Science in Systems Biology, Technical University of Munich, 85354 Freising, Germany
| | - Tolga Düz
- Chair of Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
| | - Markus Hoffmann
- Data Science in Systems Biology, Technical University of Munich, 85354 Freising, Germany
- Institute for Advanced Study, Technical University of Munich, Garching D-85748, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lina-Liv Willruth
- Data Science in Systems Biology, Technical University of Munich, 85354 Freising, Germany
| | - Jan Baumbach
- Chair of Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
- Institute of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5000 Odense, Denmark
| | - Markus List
- Data Science in Systems Biology, Technical University of Munich, 85354 Freising, Germany
| | - Olga Tsoy
- Chair of Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
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13
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Bruhn M, Obara M, Chiyyeadu A, Costa B, Salam A, Ziegler A, Waltl I, Pavlou A, Bonifacius A, Hoffmann M, Graalmann T, Pöhlmann S, Eiz-Vesper B, Schambach A, Kalinke U. Memory B cells anticipate SARS-CoV-2 variants through somatic hypermutation. J Infect 2024; 88:57-60. [PMID: 37913848 DOI: 10.1016/j.jinf.2023.10.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023]
Affiliation(s)
- Matthias Bruhn
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Maureen Obara
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Abhishek Chiyyeadu
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Bibiana Costa
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Abdus Salam
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Annett Ziegler
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Inken Waltl
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Andreas Pavlou
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Agnes Bonifacius
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany; Faculty of Biology, Georg-August-University Göttingen, Göttingen, Germany
| | - Theresa Graalmann
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; Junior Research Group for Translational Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany; Biomedical Research in End-Stage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany; Faculty of Biology, Georg-August-University Göttingen, Göttingen, Germany
| | - Britta Eiz-Vesper
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
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14
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Stankov MV, Hoffmann M, Gutierrez Jauregui R, Cossmann A, Morillas Ramos G, Graalmann T, Winter EJ, Friedrichsen M, Ravens I, Ilievska T, Ristenpart J, Schimrock A, Willenzon S, Ahrenstorf G, Witte T, Förster R, Kempf A, Pöhlmann S, Hammerschmidt SI, Dopfer-Jablonka A, Behrens GMN. Humoral and cellular immune responses following BNT162b2 XBB.1.5 vaccination. Lancet Infect Dis 2024; 24:e1-e3. [PMID: 37995739 DOI: 10.1016/s1473-3099(23)00690-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 10/30/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023]
Affiliation(s)
- Metodi V Stankov
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Centre, Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | | | - Anne Cossmann
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Gema Morillas Ramos
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Theresa Graalmann
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; Junior Research Group for Translational Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Emily Jo Winter
- Junior Research Group for Translational Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | | | - Inga Ravens
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Tamara Ilievska
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Jasmin Ristenpart
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Anja Schimrock
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Stefanie Willenzon
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Gerrit Ahrenstorf
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Torsten Witte
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; Cluster of Excellence RESIST, Hannover Medical School, 30625 Hannover, Germany
| | - Reinhold Förster
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany; Cluster of Excellence RESIST, Hannover Medical School, 30625 Hannover, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Centre, Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Centre, Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | | | - Alexandra Dopfer-Jablonka
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
| | - Georg M N Behrens
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany; CiiM, Centre for Individualized Infection Medicine, Hannover, Germany.
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15
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Hulst M, Kant A, Harders-Westerveen J, Hoffmann M, Xie Y, Laheij C, Murk JL, Van der Poel WHM. Cross-Reactivity of Human, Wild Boar, and Farm Animal Sera from Pre- and Post-Pandemic Periods with Alpha- and Βeta-Coronaviruses (CoV), including SARS-CoV-2. Viruses 2023; 16:34. [PMID: 38257734 PMCID: PMC10821012 DOI: 10.3390/v16010034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Panels of pre- and post-pandemic farm animals, wild boar and human sera, including human sera able to neutralize SARS-CoV-2 in vitro, were tested in serological tests to determine their cross-reactivity with β- and α-CoV originating from farm animals. Sera were tested in neutralization assays with high ascending concentrations (up to 1 × 104 TCID50 units/well) of β-CoV Bovine coronavirus (BCV), SARS-CoV-2, and porcine α-CoV-transmissible gastroenteritis virus (TGEV). In addition, sera were tested for immunostaining of cells infected with β-CoV porcine hemagglutinating encephalomyelitis (PHEV). Testing revealed a significantly higher percentage of BCV neutralization (78%) for sera of humans that had experienced a SARS-CoV-2 infection (SARS-CoV-2 convalescent sera) than was observed for human pre-pandemic sera (37%). Also, 46% of these human SARS-CoV-2 convalescent sera neutralized the highest concentration of BCV (5 × 103 TCID50/well) tested, whereas only 9.6% of the pre-pandemic sera did. Largely similar percentages were observed for staining of PHEV-infected cells by these panels of human sera. Furthermore, post-pandemic sera collected from wild boars living near a densely populated area in The Netherlands also showed a higher percentage (43%) and stronger BCV neutralization than was observed for pre-pandemic sera from this area (21%) and for pre- (28%) and post-pandemic (20%) sera collected from wild boars living in a nature reserve park with limited access for the public. High percentages of BCV neutralization were observed for pre- and post-pandemic sera of cows (100%), pigs (up to 45%), sheep (36%) and rabbits (60%). However, this cross-neutralization was restricted to sera collected from specific herds or farms. TGEV was neutralized only by sera of pigs (68%) and a few wild boar sera (4.6%). None of the BCV and PHEV cross-reacting human pre-pandemic, wild boar and farm animal sera effectively neutralized SARS-CoV-2 in vitro. Preexisting antibodies in human sera effectively neutralized the animal β-CoV BCV in vitro. This cross-neutralization was boosted after humans had experienced a SARS-CoV-2 infection, indicating that SARS-CoV-2 activated a "memory" antibody response against structurally related epitopes expressed on the surface of a broad range of heterologous CoV, including β-CoV isolated from farm animals. Further research is needed to elucidate if a symptomless infection or environmental exposure to SARS-CoV-2 or another β-CoV also triggers such a "memory" antibody response in wild boars and other free-living animals.
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Affiliation(s)
- Marcel Hulst
- Department Virology & Molecular Biology, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands (J.H.-W.)
| | - Arie Kant
- Department Virology & Molecular Biology, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands (J.H.-W.)
| | - José Harders-Westerveen
- Department Virology & Molecular Biology, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands (J.H.-W.)
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center—Leibniz Institute for Primate Research, 37077 Göttingen, Germany;
- Faculty of Biology and Psychology, University Göttingen, 37073 Göttingen, Germany
| | - Yajing Xie
- Institute of Food Safety and Nutrition Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
| | | | - Jean-Luc Murk
- Microvida, Elisabeth-Tweesteden Hospital, 5022 GC Tilburg, The Netherlands;
| | - Wim H. M. Van der Poel
- Department Virology & Molecular Biology, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands (J.H.-W.)
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16
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Hecker D, Lauber M, Behjati Ardakani F, Ashrafiyan S, Manz Q, Kersting J, Hoffmann M, Schulz MH, List M. Computational tools for inferring transcription factor activity. Proteomics 2023; 23:e2200462. [PMID: 37706624 DOI: 10.1002/pmic.202200462] [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: 05/17/2023] [Revised: 08/11/2023] [Accepted: 08/22/2023] [Indexed: 09/15/2023]
Abstract
Transcription factors (TFs) are essential players in orchestrating the regulatory landscape in cells. Still, their exact modes of action and dependencies on other regulatory aspects remain elusive. Since TFs act cell type-specific and each TF has its own characteristics, untangling their regulatory interactions from an experimental point of view is laborious and convoluted. Thus, there is an ongoing development of computational tools that estimate transcription factor activity (TFA) from a variety of data modalities, either based on a mapping of TFs to their putative target genes or in a genome-wide, gene-unspecific fashion. These tools can help to gain insights into TF regulation and to prioritize candidates for experimental validation. We want to give an overview of available computational tools that estimate TFA, illustrate examples of their application, debate common result validation strategies, and discuss assumptions and concomitant limitations.
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Affiliation(s)
- Dennis Hecker
- Goethe University Frankfurt, Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, Frankfurt am Main, Germany
| | - Michael Lauber
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Fatemeh Behjati Ardakani
- Goethe University Frankfurt, Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, Frankfurt am Main, Germany
| | - Shamim Ashrafiyan
- Goethe University Frankfurt, Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, Frankfurt am Main, Germany
| | - Quirin Manz
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Johannes Kersting
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- GeneSurge GmbH, München, Germany
| | - Markus Hoffmann
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Marcel H Schulz
- Goethe University Frankfurt, Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, Frankfurt am Main, Germany
| | - Markus List
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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17
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Katzmarzyk M, Clesle DC, van den Heuvel J, Hoffmann M, Garritsen H, Pöhlmann S, Jacobsen H, Čičin-Šain L. Systematical assessment of the impact of single spike mutations of SARS-CoV-2 Omicron sub-variants on the neutralization capacity of post-vaccination sera. Front Immunol 2023; 14:1288794. [PMID: 38022629 PMCID: PMC10667444 DOI: 10.3389/fimmu.2023.1288794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The evolution of novel SARS-CoV-2 variants significantly affects vaccine effectiveness. While these effects can only be studied retrospectively, neutralizing antibody titers are most used as correlates of protection. However, studies assessing neutralizing antibody titers often show heterogeneous data. Methods To address this, we investigated assay variance and identified virus infection time and dose as factors affecting assay robustness. We next measured neutralization against Omicron sub-variants in cohorts with hybrid or vaccine induced immunity, identifying a gradient of immune escape potential. To evaluate the effect of individual mutations on this immune escape potential of Omicron variants, we systematically assessed the effect of each individual mutation specific to Omicron BA.1, BA.2, BA.2.12.1, and BA.4/5. Results We cloned a library of pseudo-viruses expressing spikes with single point mutations, and subjected it to pooled sera from vaccinated hosts, thereby identifying multiple mutations that independently affect neutralization potency. Discussion These data might help to predict antigenic features of novel viral variants carrying these mutations and support the development of broad monoclonal antibodies.
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Affiliation(s)
- Maeva Katzmarzyk
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Denise Christine Clesle
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Joop van den Heuvel
- Research Group Recombinant Protein Expression, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Henk Garritsen
- Institute for Clinical Transfusion Medicine, Klinikum Braunschweig GmbH, Braunschweig, Germany
- Fraunhofer Institute for Surface Engineering and Thin Films IST, Braunschweig, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Henning Jacobsen
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Luka Čičin-Šain
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
- Centre for Individualized Infection Medicine (CIIM), Joint Venture of Helmholtz Centre for Infection Research and Medical School Hannover, Braunschweig, Germany
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18
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Hoffmann M, Poschenrieder JM, Incudini M, Baier S, Fitz A, Maier A, Hartung M, Hoffmann C, Trummer N, Adamowicz K, Picciani M, Scheibling E, Harl MV, Lesch I, Frey H, Kayser S, Wissenberg P, Schwartz L, Hafner L, Acharya A, Hackl L, Grabert G, Lee SG, Cho G, Cloward M, Jankowski J, Lee HK, Tsoy O, Wenke N, Pedersen AG, Bønnelykke K, Mandarino A, Melograna F, Schulz L, Climente-González H, Wilhelm M, Iapichino L, Wienbrandt L, Ellinghaus D, Van Steen K, Grossi M, Furth PA, Hennighausen L, Di Pierro A, Baumbach J, Kacprowski T, List M, Blumenthal DB. Network medicine-based epistasis detection in complex diseases: ready for quantum computing. medRxiv 2023:2023.11.07.23298205. [PMID: 38076997 PMCID: PMC10705612 DOI: 10.1101/2023.11.07.23298205] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Most heritable diseases are polygenic. To comprehend the underlying genetic architecture, it is crucial to discover the clinically relevant epistatic interactions (EIs) between genomic single nucleotide polymorphisms (SNPs)1-3. Existing statistical computational methods for EI detection are mostly limited to pairs of SNPs due to the combinatorial explosion of higher-order EIs. With NeEDL (network-based epistasis detection via local search), we leverage network medicine to inform the selection of EIs that are an order of magnitude more statistically significant compared to existing tools and consist, on average, of five SNPs. We further show that this computationally demanding task can be substantially accelerated once quantum computing hardware becomes available. We apply NeEDL to eight different diseases and discover genes (affected by EIs of SNPs) that are partly known to affect the disease, additionally, these results are reproducible across independent cohorts. EIs for these eight diseases can be interactively explored in the Epistasis Disease Atlas (https://epistasis-disease-atlas.com). In summary, NeEDL is the first application that demonstrates the potential of seamlessly integrated quantum computing techniques to accelerate biomedical research. Our network medicine approach detects higher-order EIs with unprecedented statistical and biological evidence, yielding unique insights into polygenic diseases and providing a basis for the development of improved risk scores and combination therapies.
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Affiliation(s)
- Markus Hoffmann
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
- Institute for Advanced Study (Lichtenbergstrasse 2 a, D-85748 Garching, Germany), Technical University of Munich, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Julian M. Poschenrieder
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
- Institute for Computational Systems Biology, University of Hamburg, Germany
| | - Massimiliano Incudini
- Dipartimento di Informatica, Universit’a di Verona, Strada le Grazie 15 - 34137, Verona, Italy
| | - Sylvie Baier
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - Amelie Fitz
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, DTU, 2800 Kgs. Lyngby, Denmark
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Maier
- Institute for Computational Systems Biology, University of Hamburg, Germany
| | - Michael Hartung
- Institute for Computational Systems Biology, University of Hamburg, Germany
| | - Christian Hoffmann
- Institute for Computational Systems Biology, University of Hamburg, Germany
| | - Nico Trummer
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - Klaudia Adamowicz
- Institute for Computational Systems Biology, University of Hamburg, Germany
| | - Mario Picciani
- Computational Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Evelyn Scheibling
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - Maximilian V. Harl
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - Ingmar Lesch
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - Hunor Frey
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - Simon Kayser
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - Paul Wissenberg
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - Leon Schwartz
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - Leon Hafner
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
- Institute for Advanced Study (Lichtenbergstrasse 2 a, D-85748 Garching, Germany), Technical University of Munich, Germany
| | - Aakriti Acharya
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics, Technische Universität Braunschweig and Hannover Medical School, Rebenring 56, 38106 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Braunschweig, Germany
| | - Lena Hackl
- Institute for Computational Systems Biology, University of Hamburg, Germany
| | - Gordon Grabert
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics, Technische Universität Braunschweig and Hannover Medical School, Rebenring 56, 38106 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Braunschweig, Germany
| | - Sung-Gwon Lee
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, Korea
| | - Gyuhyeok Cho
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Matthew Cloward
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Jakub Jankowski
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Hye Kyung Lee
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Olga Tsoy
- Institute for Computational Systems Biology, University of Hamburg, Germany
| | - Nina Wenke
- Institute for Computational Systems Biology, University of Hamburg, Germany
| | - Anders Gorm Pedersen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, DTU, 2800 Kgs. Lyngby, Denmark
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Antonio Mandarino
- International Centre for Theory of Quantum Technologies, University of Gdańsk, 80-309 Gdańsk, Poland
| | - Federico Melograna
- BIO3 - Systems Genetics; GIGA-R Medical Genomics, University of Liège, Liège, Belgium
- BIO3 - Systems Medicine; Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Laura Schulz
- Leibniz Supercomputing Centre of the Bavarian Academy of Sciences and Humanities (LRZ), Garching b. München, Germany
| | | | - Mathias Wilhelm
- Computational Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Luigi Iapichino
- Leibniz Supercomputing Centre of the Bavarian Academy of Sciences and Humanities (LRZ), Garching b. München, Germany
| | - Lars Wienbrandt
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Kristel Van Steen
- BIO3 - Systems Genetics; GIGA-R Medical Genomics, University of Liège, Liège, Belgium
- BIO3 - Systems Medicine; Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Michele Grossi
- European Organization for Nuclear Research (CERN), Geneva 1211, Switzerland
| | - Priscilla A. Furth
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
- Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA
| | - Lothar Hennighausen
- Institute for Advanced Study (Lichtenbergstrasse 2 a, D-85748 Garching, Germany), Technical University of Munich, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Alessandra Di Pierro
- Dipartimento di Informatica, Universit’a di Verona, Strada le Grazie 15 - 34137, Verona, Italy
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Germany
- Computational BioMedicine Lab, University of Southern Denmark, Denmark
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics, Technische Universität Braunschweig and Hannover Medical School, Rebenring 56, 38106 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Braunschweig, Germany
| | - Markus List
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Germany
| | - David B. Blumenthal
- Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
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19
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Hoffmann M, Willruth LL, Dietrich A, Lee HK, Knabl L, Trummer N, Baumbach J, Furth PA, Hennighausen L, List M. Blood transcriptomics analysis offers insights into variant-specific immune response to SARS-CoV-2. bioRxiv 2023:2023.11.03.564190. [PMID: 38076885 PMCID: PMC10705570 DOI: 10.1101/2023.11.03.564190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Bulk RNA sequencing (RNA-seq) of blood is typically used for gene expression analysis in biomedical research but is still rarely used in clinical practice. In this study, we argue that RNA-seq should be considered a routine diagnostic tool, as it offers not only insights into aberrant gene expression and splicing but also delivers additional readouts on immune cell type composition as well as B-cell and T-cell receptor (BCR/TCR) repertoires. We demonstrate that RNA-seq offers vital insights into a patient's immune status via integrative analysis of RNA-seq data from patients infected with various SARS-CoV-2 variants (in total 240 samples with up to 200 million reads sequencing depth). We compare the results of computational cell-type deconvolution methods (e.g., MCP-counter, xCell, EPIC, quanTIseq) to complete blood count data, the current gold standard in clinical practice. We observe varying levels of lymphocyte depletion and significant differences in neutrophil levels between SARS-CoV-2 variants. Additionally, we identify B and T cell receptor (BCR/TCR) sequences using the tools MiXCR and TRUST4 to show that - combined with sequence alignments and pBLAST - they could be used to classify a patient's disease. Finally, we investigated the sequencing depth required for such analyses and concluded that 10 million reads per sample is sufficient. In conclusion, our study reveals that computational cell-type deconvolution and BCR/TCR methods using bulk RNA-seq analyses can supplement missing CBC data and offer insights into immune responses, disease severity, and pathogen-specific immunity, all achievable with a sequencing depth of 10 million reads per sample.
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Affiliation(s)
- Markus Hoffmann
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Institute for Advanced Study (Lichtenbergstrasse 2 a, D-85748 Garching, Germany), Technical University of Munich, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Lina-Liv Willruth
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Alexander Dietrich
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Hye Kyung Lee
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | | | - Nico Trummer
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Jan Baumbach
- Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Computational BioMedicine Lab, University of Southern Denmark, Odense, Denmark
| | - Priscilla A. Furth
- Institute for Advanced Study (Lichtenbergstrasse 2 a, D-85748 Garching, Germany), Technical University of Munich, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
- Departments of Oncology & Medicine, Georgetown University, Washington, DC, United States of America
| | - Lothar Hennighausen
- Institute for Advanced Study (Lichtenbergstrasse 2 a, D-85748 Garching, Germany), Technical University of Munich, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Markus List
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
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20
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Zhang L, Kempf A, Nehlmeier I, Cossmann A, Dopfer-Jablonka A, Stankov MV, Schulz SR, Jäck HM, Behrens GMN, Pöhlmann S, Hoffmann M. Neutralisation sensitivity of SARS-CoV-2 lineages EG.5.1 and XBB.2.3. Lancet Infect Dis 2023; 23:e391-e392. [PMID: 37716358 DOI: 10.1016/s1473-3099(23)00547-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/18/2023]
Affiliation(s)
- Lu Zhang
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany
| | - Anne Cossmann
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Alexandra Dopfer-Jablonka
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; German Centre for Infection Research, partner site Hannover-Braunschweig, Hannover, Germany
| | - Metodi V Stankov
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Sebastian R Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Georg M N Behrens
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; German Centre for Infection Research, partner site Hannover-Braunschweig, Hannover, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany.
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21
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Taucher C, Lazarus R, Dellago H, Maurer G, Weisova P, Corbic-Ramljak I, Dubischar K, Lilja A, Eder-Lingelbach S, Hochreiter R, Jaramillo JC, Junker H, Krammer M, Pusic P, Querton B, Larcher-Senn J, Hoffmann M, Pöhlmann S, Finn A. Safety and immunogenicity against ancestral, Delta and Omicron virus variants following a booster dose of an inactivated whole-virus COVID-19 vaccine (VLA2001): Interim analysis of an open-label extension of the randomized, controlled, phase 3 COV-COMPARE trial. J Infect 2023; 87:242-254. [PMID: 37406777 DOI: 10.1016/j.jinf.2023.06.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 05/04/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/07/2023]
Abstract
OBJECTIVES Booster doses for COVID-19 vaccinations have been shown to amplify the waning immune response after primary vaccination and to enhance protection against emerging variants of concern (VoCs). Here, we aimed to assess the immunogenicity and safety of a booster dose of an inactivated whole-virus COVID-19 vaccine (VLA2001) after primary vaccination with 2 doses of either VLA2001 or ChAdOx1-S (Oxford-Astra Zeneca), including the cross-neutralization capacity against the Delta and Omicron VoCs. METHODS This interim analysis of an open-label extension of a randomized, controlled phase 3 trial assessed a single booster dose of an inactivated whole-virus COVID-19 vaccine (VLA2001) in healthy or medically stable adults aged 18 years and above, recruited in 21 clinical sites in the UK, who had previously received two doses of either VLA2001 or ChAdOx1-S. Safety outcomes were frequency and severity of solicited injection site and systemic reactions within 7 days after booster vaccination as well as frequency and severity of any unsolicited adverse events (AE) after up to 6 months. Immunogenicity outcomes were the immune response to ancestral SARS-CoV-2 assessed 14 days post booster expressed as geometric mean titres (GMT), GMT fold ratios and seroconversion of specific neutralizing antibodies and S-protein binding IgG antibodies. Immunogenicity against the Delta and Omicron VoCs was assessed as a post-hoc outcome with a pseudovirus neutralization antibody assay. This study is registered with ClinicalTrials.gov, NCT04864561, and is ongoing. RESULTS A booster dose of VLA2001 was administered to 958 participants, of whom 712 had been primed with VLA2001, and 246 with ChAdOx1-S. Within 7 days following these booster doses, 607 (63.4%) participants reported solicited injection site reactions, and 487 (50.8%) reported solicited systemic reactions. Up to 14 days post booster, 751 (78.4%) participants reported at least one adverse event. The tolerability profile of a booster dose of VLA2001 was similar in VLA2001-primed and ChAdOx1-S-primed participants. In VLA2001-primed participants, the GMT (95% CI) of neutralizing antibodies increased from 32.5 (22.8, 46.3) immediately before to 521.5 (413.0, 658.6) 2 weeks after administration of the booster dose, this corresponds to a geometric mean fold rise (GMFR) of 27.7 (20.0, 38.5). Compared to 2 weeks after the second priming dose, the GMFR was 3.6 (2.8, 4.7). In the ChAdOx1-S primed group, the GMT (95% CI) of neutralizing antibodies increased from 65.8 (43.9, 98.4) immediately before to 188.3 (140.3, 252.8) 2 weeks after administration of the booster dose, a geometric mean fold rise (GMFR) of 3.0 (2.2, 4.0). Compared to 2 weeks after the second priming dose, the GMFR was 1.6 (1.1, 2.2). For S-protein binding IgG antibodies, the pre- versus post-booster GMT fold ratio (95% CI) was 34.6 (25.0, 48.0) in the VLA2001-primed group and 4.0 (3.0, 5.2) in the ChAdOx1-S-primed group. Compared to 2 weeks after the second priming dose, the GMT fold rise of IgG antibodies was 3.8 (3.2, 4.6) in the VLA2001-primed group and 1.2 (0.9, 1.6) in the ChAdOx1-S-primed group. The GMT against Delta (B.1.617.2) and Omicron (BA.4/5) increased from 4.2 to 260, and from 2.7 to 56.7, respectively, when boosting subjects previously primed with VLA2001. Following the boost, 97% of subjects primed with VLA2001 had detectable Delta- and 94% Omicron-neutralizing antibodies. In subjects primed with ChAdOx1-S, the GMT against Delta and Omicron titres increased from 9.1 to 92.5, and from 3.6 to 12.3, respectively. After boosting, 99% of subjects primed with ChAdOx1-S had detectable Delta- and 70% Omicron-neutralizing antibodies. In both VLA2001 and ChAdOx1-S primed subjects, the additional VLA2001 dose boosted T cell responses against SARS-CoV-2 antigens to levels above those observed before the booster dose. CONCLUSION A booster dose of VLA2001 was safe and well tolerated after primary immunization with VLA2001 and ChAdOx1-S. The tolerability of a booster dose of VLA2001 was similar to the favourable profile observed after the first and second priming doses. Both in a homologous and a heterologous setting, boosting resulted in higher neutralizing antibody titres than after primary immunization and significant increases in cross-neutralization titres against Delta and Omicron were observed after the booster dose. These data support the use of VLA2001 in booster programmes in ChadOx1-S primed groups.
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Affiliation(s)
| | - Rajeka Lazarus
- University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Julian Larcher-Senn
- Assign Data Management and Biostatistics GmbH, Stadlweg 23, 6020 Innsbruck, Austria
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Adam Finn
- University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK; Bristol Vaccine Centre, Schools of Population Health Sciences and Cellular and Molecular Medicine, University of Bristol, Bristol, UK
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22
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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: 11] [Impact Index Per Article: 11.0] [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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23
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Gerdes S, Hoffmann M, Asadullah K, Korge B, Mortazawi D, Krüger N, Personke Y, Tabori S, Gomez M, Wegner S, Kreimendahl F, Taut F, Sticherling M. Effectiveness, safety and quality-of-life effects of guselkumab and ustekinumab in patients with psoriasis: Week 104 results from the non-interventional, prospective, German multicentre PERSIST study. J Eur Acad Dermatol Venereol 2023. [PMID: 37462295 DOI: 10.1111/jdv.19296] [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: 11/23/2022] [Accepted: 05/03/2023] [Indexed: 07/26/2023]
Abstract
BACKGROUND PERSIST was a prospective, non-interventional, real-world study of guselkumab and ustekinumab in adult patients with moderate-to-severe plaque psoriasis in Germany. OBJECTIVES To examine effectiveness, safety and quality-of-life (QoL) outcomes to Week (W) 104 of treatment with guselkumab and ustekinumab in patients with moderate-to-severe plaque psoriasis. METHODS Patients (≥18 years of age) received guselkumab or ustekinumab as per routine clinical practice. Outcomes to W104 were examined separately in guselkumab and ustekinumab recipients. An ad hoc exploratory analysis of outcomes with guselkumab versus ustekinumab was also performed following propensity score matching. RESULTS Overall, 302 and 313 patients received guselkumab and ustekinumab, respectively. Patients in both cohorts experienced improvements in disease activity and QoL that were maintained to W104, with 64.7% and 63.6% of guselkumab- and 54.6% and 64.4% of ustekinumab-treated patients achieving a Psoriasis Area and Severity Index (PASI) 90 response and a Dermatology Life Quality Index (DLQI) 0/1 score, respectively. Propensity score matching yielded well-balanced baseline characteristics except for prior biologic use, which was higher in guselkumab versus ustekinumab recipients (51.7% vs. 32.0%). Achievement of PASI ≤1 at W104 was more common in guselkumab versus ustekinumab recipients (58.7% vs. 49.7%). The W104 PASI90 response rate was 65.6% with guselkumab and 56.0% with ustekinumab; corresponding rates for PASI100 were 44.3% and 28.5%. In guselkumab recipients, response rates were higher in biologic-naïve versus biologic-experienced patients (PASI90, 77.1% vs. 53.4%; PASI100, 55.0% vs. 33.0%). A high level of response for QoL outcomes was observed for both treatments. CONCLUSIONS Ustekinumab and guselkumab led to improvements in physician-assessed and patient-reported outcomes that were sustained for up to 2 years, with no new safety signals identified. Following propensity score matching, greater improvements in PASI outcomes were observed with guselkumab versus ustekinumab. Improvements with guselkumab were highest in biologic-naïve patients, highlighting the value of early treatment.
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Affiliation(s)
- S Gerdes
- Psoriasis-Center Kiel, Department of Dermatology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - M Hoffmann
- Dermatology Practice Dr. Matthias Hoffmann, Witten, Germany
| | - K Asadullah
- Department of Dermatology, Venereology and Allergology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Prof. Dr. med. Asadullah, Dermatology Practice, Potsdam, Germany
| | - B Korge
- Dermatology Practice Dr. Bernhard Korge, Düren, Germany
| | - D Mortazawi
- Dermatology Practice Dr. Dariusch Mortazawi, Remscheid, Germany
| | - N Krüger
- Janssen-Cilag GmbH, MAF, Neuss, Germany
| | | | - S Tabori
- Janssen-Cilag GmbH, MAF, Neuss, Germany
| | - M Gomez
- Janssen Global Services LLC, Raritan, New Jersey, USA
| | - S Wegner
- Janssen-Cilag GmbH, MAF, Neuss, Germany
| | | | - F Taut
- Taut Science and Service GmbH, Konstanz, Germany
| | - M Sticherling
- Department of Dermatology, University Hospital of Erlangen, Deutsches Zentrum für Immuntherapie, Erlangen, Germany
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24
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Hoffmann M, Schwartz L, Ciora OA, Trummer N, Willruth LL, Jankowski J, Lee HK, Baumbach J, Furth PA, Hennighausen L, List M. circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging. Bioinform Adv 2023; 3:vbad093. [PMID: 37485422 PMCID: PMC10359604 DOI: 10.1093/bioadv/vbad093] [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] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023]
Abstract
Motivation Circular RNAs (circRNAs) are long noncoding RNAs (lncRNAs) often associated with diseases and considered potential biomarkers for diagnosis and treatment. Among other functions, circRNAs have been shown to act as microRNA (miRNA) sponges, preventing the role of miRNAs that repress their targets. However, there is no pipeline to systematically assess the sponging potential of circRNAs. Results We developed circRNA-sponging, a nextflow pipeline that (i) identifies circRNAs via backsplicing junctions detected in RNA-seq data, (ii) quantifies their expression values in relation to their linear counterparts spliced from the same gene, (iii) performs differential expression analysis, (iv) identifies and quantifies miRNA expression from miRNA-sequencing (miRNA-seq) data, (v) predicts miRNA binding sites on circRNAs, (vi) systematically investigates potential circRNA-miRNA sponging events, (vii) creates a network of competing endogenous RNAs and (viii) identifies potential circRNA biomarkers. We showed the functionality of the circRNA-sponging pipeline using RNA sequencing data from brain tissues, where we identified two distinct types of circRNAs characterized by a specific ratio of the number of the binding site to the length of the transcript. The circRNA-sponging pipeline is the first end-to-end pipeline to identify circRNAs and their sponging systematically with raw total RNA-seq and miRNA-seq files, allowing us to better indicate the functional impact of circRNAs as a routine aspect in transcriptomic research. Availability and implementation https://github.com/biomedbigdata/circRNA-sponging. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | | | | | - Nico Trummer
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising D-85354, Germany
| | - Lina-Liv Willruth
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising D-85354, Germany
| | - Jakub Jankowski
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jan Baumbach
- Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Computational BioMedicine Lab, University of Southern Denmark, Odense, Denmark
| | - Priscilla A Furth
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA
| | - Lothar Hennighausen
- Institute for Advanced Study, Technical University of Munich, Garching D-85748, Germany
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Markus List
- To whom correspondence should be addressed. or
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25
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Abdullah L, Nkiliza A, Niedospial D, Aldrich G, Bartenfelder G, Keegan A, Hoffmann M, Mullan M, Klimas N, Baraniuk J, Crawford F, Krengel M, Chao L, Sullivan K. Genetic association between the APOE ε4 allele, toxicant exposures and Gulf war illness diagnosis. Environ Health 2023; 22:51. [PMID: 37415220 PMCID: PMC10324249 DOI: 10.1186/s12940-023-01002-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: 04/13/2023] [Accepted: 06/28/2023] [Indexed: 07/08/2023]
Abstract
INTRODUCTION Exposure to nerve agents, pyridostigmine bromide (PB), pesticides, and oil-well fires during the 1991 Gulf War (GW) are major contributors to the etiology of Gulf War Illness (GWI). Since the apolipoprotein E (APOE) ε4 allele is associated with the risk of cognitive decline with age, particularly in the presence of environmental exposures, and cognitive impairment is one of the most common symptoms experienced by veterans with GWI, we examined whether the ε4 allele was associated with GWI. METHODS Using a case-control design, we obtained data on APOE genotypes, demographics, and self-reported GW exposures and symptoms that were deposited in the Boston Biorepository and Integrative Network (BBRAIN) for veterans diagnosed with GWI (n = 220) and healthy GW control veterans (n = 131). Diagnosis of GWI was performed using the Kansas and/or Center for Disease Control (CDC) criteria. RESULTS Age- and sex-adjusted analyses showed a significantly higher odds ratio for meeting the GWI case criteria in the presence of the ε4 allele (Odds ratio [OR] = 1.84, 95% confidence interval [CI = 1.07-3.15], p ≤ 0.05) and with two copies of the ε4 allele (OR = 1.99, 95% CI [1.23-3.21], p ≤ 0.01). Combined exposure to pesticides and PB pills (OR = 4.10 [2.12-7.91], p ≤ 0.05) as well as chemical alarms and PB pills (OR = 3.30 [1.56-6.97] p ≤ 0.05) during the war were also associated with a higher odds ratio for meeting GWI case criteria. There was also an interaction between the ε4 allele and exposure to oil well fires (OR = 2.46, 95% CI [1.07-5.62], p ≤ 0.05) among those who met the GWI case criteria. CONCLUSION These findings suggest that the presence of the ε4 allele was associated with meeting the GWI case criteria. Gulf War veterans who reported exposure to oil well fires and have an ε4 allele were more likely to meet GWI case criteria. Long-term surveillance of veterans with GWI, particularly those with oil well fire exposure, is required to better assess the future risk of cognitive decline among this vulnerable population.
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Affiliation(s)
- L Abdullah
- Roskamp Institute, Sarasota, FL, USA.
- James A. Haley VA Hospital, Tampa, FL, USA.
| | - A Nkiliza
- James A. Haley VA Hospital, Tampa, FL, USA
| | | | - G Aldrich
- Roskamp Institute, Sarasota, FL, USA
- James A. Haley VA Hospital, Tampa, FL, USA
| | | | - A Keegan
- Roskamp Institute, Sarasota, FL, USA
| | | | - M Mullan
- Roskamp Institute, Sarasota, FL, USA
| | - N Klimas
- Nova Southeastern University, Ft Lauderdale, FL, USA
- Miami VA Medical Center GRECC, Miami, FL, USA
| | - J Baraniuk
- Department of Medicine, Georgetown University, Washington, DC, USA
| | - F Crawford
- Roskamp Institute, Sarasota, FL, USA
- James A. Haley VA Hospital, Tampa, FL, USA
| | - M Krengel
- Boston University School of Medicine, Boston, MA, USA
| | - L Chao
- University of California, San Francisco, CA, USA
| | - K Sullivan
- Boston University School of Public Health, Boston, MA, USA
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26
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Maier A, Hartung M, Abovsky M, Adamowicz K, Bader GD, Baier S, Blumenthal DB, Chen J, Elkjaer ML, Garcia-Hernandez C, Helmy M, Hoffmann M, Jurisica I, Kotlyar M, Lazareva O, Levi H, List M, Lobentanzer S, Loscalzo J, Malod-Dognin N, Manz Q, Matschinske J, Mee M, Oubounyt M, Pico AR, Pillich RT, Poschenrieder JM, Pratt D, Pržulj N, Sadegh S, Saez-Rodriguez J, Sarkar S, Shaked G, Shamir R, Trummer N, Turhan U, Wang R, Zolotareva O, Baumbach J. Drugst.One - A plug-and-play solution for online systems medicine and network-based drug repurposing. ArXiv 2023:arXiv:2305.15453v2. [PMID: 37332567 PMCID: PMC10274948] [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] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood. In response, computational systems and network medicine tools have emerged to identify potential drug repurposing candidates. However, these tools often require complex installation and lack intuitive visual network mining capabilities. To tackle these challenges, we introduce Drugst.One, a platform that assists specialized computational medicine tools in becoming user-friendly, web-based utilities for drug repurposing. With just three lines of code, Drugst.One turns any systems biology software into an interactive web tool for modeling and analyzing complex protein-drug-disease networks. Demonstrating its broad adaptability, Drugst.One has been successfully integrated with 21 computational systems medicine tools. Available at https://drugst.one, Drugst.One has significant potential for streamlining the drug discovery process, allowing researchers to focus on essential aspects of pharmaceutical treatment research.
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Affiliation(s)
- Andreas Maier
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Michael Hartung
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Mark Abovsky
- Division of Orthopaedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre, Osteoarthritis Research Program, Krembil Research Institute, UHN, Toronto, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, 60 Leonard Avenue, 5KD-407, Toronto, ON, M5T 0S8, Canada
| | - Klaudia Adamowicz
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Gary D Bader
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Sylvie Baier
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - David B Blumenthal
- Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91052 Erlangen, Germany
| | - Jing Chen
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Maria L Elkjaer
- Department of Neurology, Odense University Hospital, Odense, Denmark
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | | | - Mohamed Helmy
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Markus Hoffmann
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Institute for Advanced Study (Lichtenbergstrasse 2a, D-85748 Garching, Germany), Technical University of Munich, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Igor Jurisica
- Division of Orthopaedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre, Osteoarthritis Research Program, Krembil Research Institute, UHN, Toronto, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, 60 Leonard Avenue, 5KD-407, Toronto, ON, M5T 0S8, Canada
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Max Kotlyar
- Division of Orthopaedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre, Osteoarthritis Research Program, Krembil Research Institute, UHN, Toronto, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, 60 Leonard Avenue, 5KD-407, Toronto, ON, M5T 0S8, Canada
| | - Olga Lazareva
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Junior Clinical Cooperation Unit Multiparametric methods for early detection of prostate cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Hagai Levi
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Markus List
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Sebastian Lobentanzer
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Quirin Manz
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Julian Matschinske
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Miles Mee
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Mhaned Oubounyt
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Alexander R Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, 1650 Owens Street, San Francisco, 94158, California, USA
| | - Rudolf T Pillich
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Julian M Poschenrieder
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Dexter Pratt
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Nataša Pržulj
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Department of Computer Science, University College London, London WC1E 6BT, UK
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Sepideh Sadegh
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Suryadipto Sarkar
- Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91052 Erlangen, Germany
| | - Gideon Shaked
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Nico Trummer
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Ugur Turhan
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Ruisheng Wang
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Olga Zolotareva
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Computational Biomedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
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27
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Weiss ML, Domschikowski J, Krug D, Sonnhoff M, Nitsche M, Hoffmann W, Becker-Schiebe M, Bock F, Hoffmann M, Schmalz C, Dunst J, Fabian A. The impact of palliative radiotherapy on health-related quality of life in patients with head and neck cancer - Results of a multicenter prospective cohort study. Clin Transl Radiat Oncol 2023; 41:100633. [PMID: 37206410 PMCID: PMC10189372 DOI: 10.1016/j.ctro.2023.100633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/13/2023] [Accepted: 04/24/2023] [Indexed: 05/21/2023] Open
Abstract
Purpose Palliative radiotherapy for patients with head and neck cancer can be used to alleviate symptoms. Only a few studies have investigated its impact on patient-reported outcomes (PRO). Therefore, we conducted a prospective multicenter observational study. The primary objective was to assess changes in health-related quality of life (HrQoL) per PRO. Methods Eligibility criteria included i.) head and neck cancer and ii.) palliative radiotherapy indicated (EQD2Gy < 60 Gy). The primary follow-up date was eight weeks after radiotherapy (t8w). PRO measures included the EORTC QLQ-C30 and EORTC QLQ-H&N43 and pain per Numeric Rating Scale (NRS). Per protocol, five PRO domains were to be reported in detail as well as PRO domains corresponding to a primary and secondary symptom as determined by the individual patient. We defined a minimal important difference (MID) of 10 points. Results From 06/2020 to 06/2022, 61 patients were screened and 21 patients were included. Due to death or decline in health-status, HrQoL data was available for 18 patients at the first fraction and for eight patients at t8w. The MID was not met for the predefined domains in terms of mean values as compared from first fraction to t8w. Individually in those patients with available HrQoL data at t8w, 71% (5/7) improved in their primary and 40% (2/5) in their secondary symptom domain reaching the MID from first fraction to t8w, respectively. There was a significant improvement in pain per NRS in those patients with available data at t8w per Wilcoxon signed rank test (p = 0.041). Acute mucositis of grade ≥3 per CTCAE v5.0 occurred in 44% (8/18) of the patients. The median overall survival was 11 months. Conclusion Despite low patient numbers and risk of selection bias, our study shows some evidence of a benefit from palliative radiotherapy for head and neck cancer as measured by PRO.German Clinical Trial Registry identifier: DRKS00021197.
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Affiliation(s)
- Marie-Luise Weiss
- Department of Radiation Oncology, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Justus Domschikowski
- Department of Radiation Oncology, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - David Krug
- Department of Radiation Oncology, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Mathias Sonnhoff
- Center for Radiotherapy and Radiation Oncology, 28239 Bremen, Germany
| | - Mirko Nitsche
- Center for Radiotherapy and Radiation Oncology, 28239 Bremen, Germany
| | - Wolfgang Hoffmann
- Radiotherapy & Radiation Oncology, Hospital Braunschweig, 38114 Braunschweig, Germany
| | | | - Felix Bock
- Department of Radiotherapy, University of Rostock, 18059 Rostock, Germany
| | - Markus Hoffmann
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Schleswig-Holstein Campus Kiel, Germany
| | - Claudia Schmalz
- Department of Radiation Oncology, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Jürgen Dunst
- Department of Radiation Oncology, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Alexander Fabian
- Department of Radiation Oncology, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
- Corresponding author at: Department of Radiation Oncology, University Hospital Schleswig-Holstein, Arnold-Heller-Str. 3, 24105 Kiel, Germany.
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28
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Budhadev D, Hooper J, Rocha C, Nehlmeier I, Kempf AM, Hoffmann M, Krüger N, Zhou D, Pöhlmann S, Guo Y. Polyvalent Nano-Lectin Potently Neutralizes SARS-CoV-2 by Targeting Glycans on the Viral Spike Protein. JACS Au 2023; 3:1755-1766. [PMID: 37388683 PMCID: PMC10302749 DOI: 10.1021/jacsau.3c00163] [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] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 07/01/2023]
Abstract
Mutations in spike (S) protein epitopes allow SARS-CoV-2 variants to evade antibody responses induced by infection and/or vaccination. In contrast, mutations in glycosylation sites across SARS-CoV-2 variants are very rare, making glycans a potential robust target for developing antivirals. However, this target has not been adequately exploited for SARS-CoV-2, mostly due to intrinsically weak monovalent protein-glycan interactions. We hypothesize that polyvalent nano-lectins with flexibly linked carbohydrate recognition domains (CRDs) can adjust their relative positions and bind multivalently to S protein glycans, potentially exerting potent antiviral activity. Herein, we displayed the CRDs of DC-SIGN, a dendritic cell lectin known to bind to diverse viruses, polyvalently onto 13 nm gold nanoparticles (named G13-CRD). G13-CRD bound strongly and specifically to target glycan-coated quantum dots with sub-nM Kd. Moreover, G13-CRD neutralized particles pseudotyped with the S proteins of Wuhan Hu-1, B.1, Delta variant and Omicron subvariant BA.1 with low nM EC50. In contrast, natural tetrameric DC-SIGN and its G13 conjugate were ineffective. Further, G13-CRD potently inhibited authentic SARS-CoV-2 B.1 and BA.1, with <10 pM and <10 nM EC50, respectively. These results identify G13-CRD as the 1st polyvalent nano-lectin with broad activity against SARS-CoV-2 variants that merits further exploration as a novel approach to antiviral therapy.
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Affiliation(s)
- Darshita Budhadev
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - James Hooper
- School
of Food Science & Nutrition and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Cheila Rocha
- Infection
Biology Unit, German Primate Center −
Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Faculty
of Biology and Psychology, Georg-August-University
Göttingen, 37073 Göttingen, Germany
| | - Inga Nehlmeier
- Infection
Biology Unit, German Primate Center −
Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Amy Madeleine Kempf
- Infection
Biology Unit, German Primate Center −
Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Faculty
of Biology and Psychology, Georg-August-University
Göttingen, 37073 Göttingen, Germany
| | - Markus Hoffmann
- Infection
Biology Unit, German Primate Center −
Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Faculty
of Biology and Psychology, Georg-August-University
Göttingen, 37073 Göttingen, Germany
| | - Nadine Krüger
- Infection
Biology Unit, German Primate Center −
Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Dejian Zhou
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Stefan Pöhlmann
- Infection
Biology Unit, German Primate Center −
Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Faculty
of Biology and Psychology, Georg-August-University
Göttingen, 37073 Göttingen, Germany
| | - Yuan Guo
- School
of Food Science & Nutrition and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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29
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Hoffmann M, Wong LYR, Arora P, Zhang L, Rocha C, Odle A, Nehlmeier I, Kempf A, Richter A, Halwe NJ, Schön J, Ulrich L, Hoffmann D, Beer M, Drosten C, Perlman S, Pöhlmann S. Omicron subvariant BA.5 efficiently infects lung cells. Nat Commun 2023; 14:3500. [PMID: 37311762 DOI: 10.1038/s41467-023-39147-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 05/26/2023] [Indexed: 06/15/2023] Open
Abstract
The SARS-CoV-2 Omicron subvariants BA.1 and BA.2 exhibit reduced lung cell infection relative to previously circulating SARS-CoV-2 variants, which may account for their reduced pathogenicity. However, it is unclear whether lung cell infection by BA.5, which displaced these variants, remains attenuated. Here, we show that the spike (S) protein of BA.5 exhibits increased cleavage at the S1/S2 site and drives cell-cell fusion and lung cell entry with higher efficiency than its counterparts from BA.1 and BA.2. Increased lung cell entry depends on mutation H69Δ/V70Δ and is associated with efficient replication of BA.5 in cultured lung cells. Further, BA.5 replicates in the lungs of female Balb/c mice and the nasal cavity of female ferrets with much higher efficiency than BA.1. These results suggest that BA.5 has acquired the ability to efficiently infect lung cells, a prerequisite for causing severe disease, suggesting that evolution of Omicron subvariants can result in partial loss of attenuation.
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Affiliation(s)
- Markus Hoffmann
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany.
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany.
| | - Lok-Yin Roy Wong
- Departments of Microbiology and Immunology, BSB 3-712, University of Iowa, Iowa City, IA, USA
| | - Prerna Arora
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Lu Zhang
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Cheila Rocha
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Abby Odle
- Departments of Microbiology and Immunology, BSB 3-712, University of Iowa, Iowa City, IA, USA
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Anja Richter
- Institute of Virology, Charité - Universitätsmedizin Berlin, Campus Charité Mitte, Berlin, Germany
| | - Nico Joel Halwe
- Institut für Virusdiagnostik (IVD), Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Jacob Schön
- Institut für Virusdiagnostik (IVD), Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Lorenz Ulrich
- Institut für Virusdiagnostik (IVD), Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Donata Hoffmann
- Institut für Virusdiagnostik (IVD), Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Martin Beer
- Institut für Virusdiagnostik (IVD), Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, Campus Charité Mitte, Berlin, Germany
| | - Stanley Perlman
- Departments of Microbiology and Immunology, BSB 3-712, University of Iowa, Iowa City, IA, USA
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany.
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany.
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30
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Hoffmann M, Fischer MA, Neumann B, Kiesewetter K, Hoffmann I, Werner G, Pfeifer Y, Lübbert C. Carbapenemase-producing Gram-negative bacteria in hospital wastewater, wastewater treatment plants and surface waters in a metropolitan area in Germany, 2020. Sci Total Environ 2023; 890:164179. [PMID: 37201847 DOI: 10.1016/j.scitotenv.2023.164179] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/27/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023]
Abstract
Carbapenemase-producing bacteria (CPB) such as Klebsiella pneumoniae and Escherichia coli are causing hospital outbreaks worldwide. An important transfer route into the aquatic environment is the urban water cycle. We aimed to determine the presence of CPB in hospital wastewater, wastewater treatment plants (WWTPs) and surface waters in a German metropolitan area and to characterise these bacteria by whole-genome comparisons. During two periods in 2020, 366 samples were collected and cultivated on chromogenic screening media. Bacterial colonies were selected for species identification and PCR-based carbapenemase gene screening. Genomes of all detected CPB were sequenced and analysed for resistance gene content, followed by multilocus sequence typing (MLST) and core genome MLST (cgMLST) for K. pneumoniae and E. coli isolates. Carbapenemase genes were detected in 243 isolates, most of which belonged to genera/species Citrobacter spp. (n = 70), Klebsiella spp. (n = 57), Enterobacter spp. (n = 52) and E. coli (n = 42). Genes encoding KPC-2 carbapenemase were detected in 124 of 243 isolates. K. pneumoniae produced mainly KPC-2 and OXA-232 whereas E. coli harboured various enzymes (KPC-2, VIM-1, OXA-48, NDM-5, KPC-2 + OXA-232, GES-5, GES-5 + VIM-1, IMP-8 + OXA-48). Eight and twelve sequence types (STs) were identified for K. pneumoniae and E. coli, respectively, forming different clusters. The detection of numerous CPB species in hospital wastewater, WWTPs and river water is of concern. Genome data highlight a hospital-specific presence of distinct carbapenemase-producing K. pneumoniae and E. coli strains belonging to "global epidemic clones" in wastewater samples representing local epidemiology. The various detected CPB species including E. coli ST635, which is not known to cause human infections, could serve as reservoirs/vectors for the spread of carbapenemase genes in the environment. Therefore, effective pretreatment of hospital wastewater prior to discharge into the municipal wastewater system may be required, although swimming lakes do not appear to be a relevant risk factor for CPB ingestion and infection.
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Affiliation(s)
| | - Martin A Fischer
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, D-38855 Wernigerode, Germany
| | - Bernd Neumann
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, D-38855 Wernigerode, Germany; Institute for Hospital Hygiene, Medical Microbiology and Clinical Infectiology, Paracelsus Medical University, Nuremberg General Hospital, D-90419 Nuremberg, Germany
| | | | - Ines Hoffmann
- MVZ Dr. Reising-Ackermann & Colleagues, D-04289 Leipzig, Germany
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, D-38855 Wernigerode, Germany
| | - Yvonne Pfeifer
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, D-38855 Wernigerode, Germany
| | - Christoph Lübbert
- Interdisciplinary Center for Infectious Diseases, Leipzig University Medical Center, D-04103 Leipzig, Germany; Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Leipzig University Medical Center, D-04103 Leipzig, Germany.
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31
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Boniolo F, Hoffmann M, Roggendorf N, Tercan B, Baumbach J, Castro MAA, Robertson AG, Saur D, List M. spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape. Bioinformatics 2023; 39:7135833. [PMID: 37084275 DOI: 10.1093/bioinformatics/btad276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/03/2023] [Accepted: 04/17/2023] [Indexed: 04/23/2023] Open
Abstract
MOTIVATION Cancer is one of the leading causes of death worldwide. Despite significant improvements in prevention and treatment, mortality remains high for many cancer types. Hence, innovative methods that use molecular data to stratify patients and identify biomarkers are needed. Promising biomarkers can also be inferred from competing endogenous RNA (ceRNA) networks that capture the gene-miRNA gene regulatory landscape. Thus far, the role of these biomarkers could only be studied globally but not in a sample-specific manner. To mitigate this, we introduce spongEffects, a novel method that infers subnetworks (or modules) from ceRNA networks and calculates patient- or sample-specific scores related to their regulatory activity. RESULTS We show how spongEffects can be used for downstream interpretation and machine learning tasks such as tumor classification and for identifying subtype-specific regulatory interactions. In a concrete example of breast cancer subtype classification, we prioritize modules impacting the biology of the different subtypes. In summary, spongEffects prioritizes ceRNA modules as biomarkers and offers insights into the miRNA regulatory landscape. Notably, these module scores can be inferred from gene expression data alone and can thus be applied to cohorts where miRNA expression information is lacking. AVAILABILITY https://bioconductor.org/packages/devel/bioc/html/SPONGE.html. SUPPLEMENTARY DATA are available at Bioinformatics online.
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Affiliation(s)
- Fabio Boniolo
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Markus Hoffmann
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Institute for Advanced Study (Lichtenbergstrasse 2 a, D-85748 Garching, Germany), Technical University of Munich, Germany
| | - Norman Roggendorf
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | | | - Jan Baumbach
- Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Computational BioMedicine Lab, University of Southern Denmark, Odense, Denmark
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Universidade Federal do Paraná, Curitiba, Brazil
| | | | - Dieter Saur
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Markus List
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
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32
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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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Mehanna H, Taberna M, von Buchwald C, Tous S, Brooks J, Mena M, Morey F, Grønhøj C, Rasmussen JH, Garset-Zamani M, Bruni L, Batis N, Brakenhoff RH, Leemans CR, Baatenburg de Jong RJ, Klussmann JP, Wuerdemann N, Wagner S, Dalianis T, Marklund L, Mirghani H, Schache A, James JA, Huang SH, O'Sullivan B, Nankivell P, Broglie MA, Hoffmann M, Quabius ES, Alemany L, Taberna M, von Buchwald C, Tous S, Huang SH, O'Sullivan B, Garset-Zamani M, Brooks J, Batis N, Fulton-Lieuw T, Nankivell P, Schache A, James JA, Brakenhoff RH, Leemans CR, Heideman DAM, Bloemena E, Nauta I, de Jong RB, Dalianis T, Marklund L, Mirghani H, Wagner S, Wittekindt C, Klussmann JP, Wuerdemann N, Quaas A, Sharma SJ, Maltseva M, Zimmermann P, Hoffmann M, Quabius ES, Däppen MB, Ärztin L, Bruni L, Mena M, Morey F, Alemany L. Prognostic implications of p16 and HPV discordance in oropharyngeal cancer (HNCIG-EPIC-OPC): a multicentre, multinational, individual patient data analysis. Lancet Oncol 2023; 24:239-251. [PMID: 36796393 DOI: 10.1016/s1470-2045(23)00013-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND p16INK4a (p16) immunohistochemistry is the most widely used biomarker assay for inferring HPV causation in oropharyngeal cancer in clinical and trial settings. However, discordance exists between p16 and HPV DNA or RNA status in some patients with oropharyngeal cancer. We aimed to clearly quantify the extent of discordance, and its prognostic implications. METHODS In this multicentre, multinational individual patient data analysis, we did a literature search in PubMed and Cochrane database for systematic reviews and original studies published in English between Jan 1, 1970, and Sept 30, 2022. We included retrospective series and prospective cohorts of consecutively recruited patients previously analysed in individual studies with minimum cohort size of 100 patients with primary squamous cell carcinoma of the oropharynx. Patient inclusion criteria were diagnosis with a primary squamous cell carcinoma of oropharyngeal cancer; data on p16 immunohistochemistry and on HPV testing; information on age, sex, tobacco, and alcohol use; staging by TNM 7th edition; information on treatments received; and data on clinical outcomes and follow-up (date of last follow-up if alive, date of recurrence or metastasis, and date and cause of death). There were no limits on age or performance status. The primary outcomes were the proportion of patients of the overall cohort who showed the different p16 and HPV result combinations, as well as 5-year overall survival and 5-year disease-free survival. Patients with recurrent or metastatic disease or who were treated palliatively were excluded from overall survival and disease-free survival analyses. Multivariable analysis models were used to calculate adjusted hazard ratios (aHR) for different p16 and HPV testing methods for overall survival, adjusted for prespecified confounding factors. FINDINGS Our search returned 13 eligible studies that provided individual data for 13 cohorts of patients with oropharyngeal cancer from the UK, Canada, Denmark, Sweden, France, Germany, the Netherlands, Switzerland, and Spain. 7895 patients with oropharyngeal cancer were assessed for eligibility. 241 were excluded before analysis, and 7654 were eligible for p16 and HPV analysis. 5714 (74·7%) of 7654 patients were male and 1940 (25·3%) were female. Ethnicity data were not reported. 3805 patients were p16-positive, 415 (10·9%) of whom were HPV-negative. This proportion differed significantly by geographical region and was highest in the areas with lowest HPV-attributable fractions (r=-0·744, p=0·0035). The proportion of patients with p16+/HPV- oropharyngeal cancer was highest in subsites outside the tonsil and base of tongue (29·7% vs 9·0%, p<0·0001). 5-year overall survival was 81·1% (95% CI 79·5-82·7) for p16+/HPV+, 40·4% (38·6-42·4) for p16-/HPV-, 53·2% (46·6-60·8) for p16-/HPV+, and 54·7% (49·2-60·9) for p16+/HPV-. 5-year disease-free survival was 84·3% (95% CI 82·9-85·7) for p16+/HPV+, 60·8% (58·8-62·9) for p16-/HPV-; 71·1% (64·7-78·2) for p16-/HPV+, and 67·9% (62·5-73·7) for p16+/HPV-. Results were similar across all European sub-regions, but there were insufficient numbers of discordant patients from North America to draw conclusions in this cohort. INTERPRETATION Patients with discordant oropharyngeal cancer (p16-/HPV+ or p16+/HPV-) had a significantly worse prognosis than patients with p16+/HPV+ oropharyngeal cancer, and a significantly better prognosis than patients with p16-/HPV- oropharyngeal cancer. Along with routine p16 immunohistochemistry, HPV testing should be mandated for clinical trials for all patients (or at least following a positive p16 test), and is recommended where HPV status might influence patient care, especially in areas with low HPV-attributable fractions. FUNDING European Regional Development Fund, Generalitat de Catalunya, National Institute for Health Research (NIHR) UK, Cancer Research UK, Medical Research Council UK, and The Swedish Cancer Foundation and the Stockholm Cancer Society.
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Affiliation(s)
- Hisham Mehanna
- Institute of Head and Neck Studies and Education (InHANSE), Institute of Cancer and Genomics Sciences, University of Birmingham, Birmingham, UK.
| | - Miren Taberna
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Cancer Epidemiology Research Programme, Catalan Institute of Oncology (ICO), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Department of Medicine, University of Barcelona, Barcelona, Spain
| | - Christian von Buchwald
- Department of Otolaryngology, Head and Neck Surgery and Audiology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Sara Tous
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology (ICO), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Epidemiology and Public Health, Centro de Investigación Biomédica en Red: Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Jill Brooks
- Institute of Head and Neck Studies and Education (InHANSE), Institute of Cancer and Genomics Sciences, University of Birmingham, Birmingham, UK
| | - Marisa Mena
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology (ICO), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Epidemiology and Public Health, Centro de Investigación Biomédica en Red: Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Francisca Morey
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology (ICO), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Christian Grønhøj
- Department of Otolaryngology, Head and Neck Surgery and Audiology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Jacob Høygaard Rasmussen
- Department of Otolaryngology, Head and Neck Surgery and Audiology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Martin Garset-Zamani
- Department of Otolaryngology, Head and Neck Surgery and Audiology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Laia Bruni
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology (ICO), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Epidemiology and Public Health, Centro de Investigación Biomédica en Red: Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Nikolaos Batis
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology (ICO), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ruud H Brakenhoff
- Otolaryngology-head and neck surgery, Cancer Centre Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Netherlands
| | - C René Leemans
- Otolaryngology-head and neck surgery, Cancer Centre Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Netherlands
| | | | - Jens Peter Klussmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Cologne, Cologne, Germany
| | - Nora Wuerdemann
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Cologne, Cologne, Germany
| | - Steffen Wagner
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Giessen, Germany
| | - Tina Dalianis
- Department of Oncology-Pathology, Karolinska University Hospital, Stockholm, Sweden
| | - Linda Marklund
- Department of Clinical Science, Intervention and Technology, Department of Oto-Rhinolaryngology, Head and Neck Surgery, Karolinska University Hospital, Stockholm, Sweden; Medical Unit Head and Neck, Lung and Skin Cancer, Karolinska University Hospital, Stockholm, Sweden; Department of Surgical Sciences, Section of Otolaryngology and Head and Neck Surgery, Uppsala University, Uppsala, Sweden
| | - Haïtham Mirghani
- Department of Head and Neck Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Andrew Schache
- Liverpool Head & Neck Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Jaqueline A James
- Precision Medicine Centre of Excellence, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, UK; Regional Molecular Diagnostic Service, Belfast Health and Social Care Trust, Belfast, Northern Ireland, UK
| | - Shao Hui Huang
- Department of Radiation Oncology/Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Brian O'Sullivan
- Department of Radiation Oncology/Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Paul Nankivell
- Institute of Head and Neck Studies and Education (InHANSE), Institute of Cancer and Genomics Sciences, University of Birmingham, Birmingham, UK
| | - Martina A Broglie
- Department of Otorhinolaryngology-Head and Neck Surgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Markus Hoffmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Elgar Susanne Quabius
- Department of Otorhinolaryngology, Head and Neck Surgery, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Laia Alemany
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology (ICO), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Epidemiology and Public Health, Centro de Investigación Biomédica en Red: Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
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Labarile M, Loosli T, Zeeb M, Kusejko K, Huber M, Hirsch HH, Perreau M, Ramette A, Yerly S, Cavassini M, Battegay M, Rauch A, Calmy A, Notter J, Bernasconi E, Fux C, Günthard HF, Pasin C, Kouyos RD, Aebi-Popp K, Anagnostopoulos A, Battegay M, Bernasconi E, Braun DL, Bucher HC, Calmy A, Cavassini M, Ciuffi A, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Günthard HF, Hachfeld A, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Huber M, Kahlert CR, Kaiser L, Keiser O, Klimkait T, Kouyos RD, Kovari H, Kusejko K, Martinetti G, Martinez de Tejada B, Marzolini C, Metzner KJ, Müller N, Nemeth J, Nicca D, Paioni P, Pantaleo G, Perreau M, Rauch A, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Wandeler G, Yerly S. Quantifying and Predicting Ongoing Human Immunodeficiency Virus Type 1 Transmission Dynamics in Switzerland Using a Distance-Based Clustering Approach. J Infect Dis 2023; 227:554-564. [PMID: 36433831 DOI: 10.1093/infdis/jiac457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/11/2022] [Accepted: 11/25/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Despite effective prevention approaches, ongoing human immunodeficiency virus 1 (HIV-1) transmission remains a public health concern indicating a need for identifying its drivers. METHODS We combined a network-based clustering method using evolutionary distances between viral sequences with statistical learning approaches to investigate the dynamics of HIV transmission in the Swiss HIV Cohort Study and to predict the drivers of ongoing transmission. RESULTS We found that only a minority of clusters and patients acquired links to new infections between 2007 and 2020. While the growth of clusters and the probability of individual patients acquiring new links in the transmission network was associated with epidemiological, behavioral, and virological predictors, the strength of these associations decreased substantially when adjusting for network characteristics. Thus, these network characteristics can capture major heterogeneities beyond classical epidemiological parameters. When modeling the probability of a newly diagnosed patient being linked with future infections, we found that the best predictive performance (median area under the curve receiver operating characteristic AUCROC = 0.77) was achieved by models including characteristics of the network as predictors and that models excluding them performed substantially worse (median AUCROC = 0.54). CONCLUSIONS These results highlight the utility of molecular epidemiology-based network approaches for analyzing and predicting ongoing HIV transmission dynamics. This approach may serve for real-time prospective assessment of HIV transmission.
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Affiliation(s)
- Marco Labarile
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Tom Loosli
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Marius Zeeb
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Hans H Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland.,Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Sabine Yerly
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Manuel Battegay
- Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Alexandra Calmy
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Julia Notter
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Christoph Fux
- Department of Infectious Diseases, Kantonsspital Aarau, Aarau, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Chloé Pasin
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Shilts J, Crozier TWM, Teixeira-Silva A, Gabaev I, Gerber PP, Greenwood EJD, Watson SJ, Ortmann BM, Gawden-Bone CM, Pauzaite T, Hoffmann M, Nathan JA, Pöhlmann S, Matheson NJ, Lehner PJ, Wright GJ. LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein. PLoS Biol 2023; 21:e3001959. [PMID: 36735681 PMCID: PMC9897555 DOI: 10.1371/journal.pbio.3001959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/14/2022] [Indexed: 02/04/2023] Open
Abstract
The interactions between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and human host factors enable the virus to propagate infections that lead to Coronavirus Disease 2019 (COVID-19). The spike protein is the largest structural component of the virus and mediates interactions essential for infection, including with the primary angiotensin-converting enzyme 2 (ACE2) receptor. We performed two independent cell-based systematic screens to determine whether there are additional proteins by which the spike protein of SARS-CoV-2 can interact with human cells. We discovered that in addition to ACE2, expression of LRRC15 also causes spike protein binding. This interaction is distinct from other known spike attachment mechanisms such as heparan sulfates or lectin receptors. Measurements of orthologous coronavirus spike proteins implied the interaction was functionally restricted to SARS-CoV-2 by accessibility. We localized the interaction to the C-terminus of the S1 domain and showed that LRRC15 shares recognition of the ACE2 receptor binding domain. From analyzing proteomics and single-cell transcriptomics, we identify LRRC15 expression as being common in human lung vasculature cells and fibroblasts. Levels of LRRC15 were greatly elevated by inflammatory signals in the lungs of COVID-19 patients. Although infection assays demonstrated that LRRC15 alone is not sufficient to permit viral entry, we present evidence that it can modulate infection of human cells. This unexpected interaction merits further investigation to determine how SARS-CoV-2 exploits host LRRC15 and whether it could account for any of the distinctive features of COVID-19.
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Affiliation(s)
- Jarrod Shilts
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Thomas W. M. Crozier
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Ana Teixeira-Silva
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Ildar Gabaev
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Pehuén Pereyra Gerber
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Edward J. D. Greenwood
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Samuel James Watson
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Brian M. Ortmann
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Christian M. Gawden-Bone
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Tekle Pauzaite
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center – Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August University Göttingen, Göttingen, Germany
| | - James A. Nathan
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center – Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August University Göttingen, Göttingen, Germany
| | - Nicholas J. Matheson
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
| | - Paul J. Lehner
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Gavin J. Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom
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Hoffmann M, Schwartz L, Ciora OA, Trummer N, Willruth LL, Jankowski J, Lee HK, Baumbach J, Furth P, Hennighausen L, List M. circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging. bioRxiv 2023:2023.01.19.524495. [PMID: 36789427 PMCID: PMC9928029 DOI: 10.1101/2023.01.19.524495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Motivation Circular RNAs (circRNAs) are long non-coding RNAs (lncRNAs) often associated with diseases and considered potential biomarkers for diagnosis and treatment. Among other functions, circRNAs have been shown to act as microRNA (miRNA) sponges, preventing the role of miRNAs that repress their targets. However, there is no pipeline to systematically assess the sponging potential of circRNAs. Results We developed circRNA-sponging, a nextflow pipeline that (1) identifies circRNAs via back-splicing junctions detected in RNA-seq data, (2) quantifies their expression values in relation to their linear counterparts spliced from the same gene, (3) performs differential expression analysis, (4) identifies and quantifies miRNA expression from miRNA-sequencing (miRNA-seq) data, (5) predicts miRNA binding sites on circRNAs, (6) systematically investigates potential circRNA-miRNA sponging events, (7) creates a network of competing endogenous RNAs, and (8) identifies potential circRNA biomarkers. We showed the functionality of the circRNA-sponging pipeline using RNA sequencing data from brain tissues where we identified two distinct types of circRNAs characterized by a distinct ratio of the binding site length. The circRNA-sponging pipeline is the first end-to-end pipeline to identify circRNAs and their sponging systematically with raw total RNA-seq and miRNA-seq files, allowing us to better indicate the functional impact of circRNAs as a routine aspect in transcriptomic research. Availability https://github.com/biomedbigdata/circRNA-sponging. Contact markus.daniel.hoffmann@tum.de ; markus.list@tum.de. Supplementary Material Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Markus Hoffmann
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany,Institute for Advanced Study (Lichtenbergstrasse 2a, D-85748 Garching, Germany), Technical University of Munich, Germany,National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America,corresponding authors Contact:;
| | - Leon Schwartz
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Octavia-Andreea Ciora
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Nico Trummer
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Lina-Liv Willruth
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Jakub Jankowski
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Hye Kyung Lee
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Jan Baumbach
- Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany,Computational BioMedicine Lab, University of Southern Denmark, Odense, Denmark
| | - Priscilla Furth
- Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA
| | - Lothar Hennighausen
- Institute for Advanced Study (Lichtenbergstrasse 2a, D-85748 Garching, Germany), Technical University of Munich, Germany,National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Markus List
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany,corresponding authors Contact:;
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Wettstein L, Immenschuh P, Weil T, Conzelmann C, Almeida‐Hernández Y, Hoffmann M, Kempf A, Nehlmeier I, Lotke R, Petersen M, Stenger S, Kirchhoff F, Sauter D, Pöhlmann S, Sanchez‐Garcia E, Münch J. Inside Back Cover Image, Volume 95, Number 1, January 2023. J Med Virol 2023. [DOI: 10.1002/jmv.28468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Lukas Wettstein
- Institute of Molecular Virology Ulm University Medical Center Ulm Germany
| | - Patrick Immenschuh
- Institute of Molecular Virology Ulm University Medical Center Ulm Germany
| | - Tatjana Weil
- Institute of Molecular Virology Ulm University Medical Center Ulm Germany
| | - Carina Conzelmann
- Institute of Molecular Virology Ulm University Medical Center Ulm Germany
| | - Yasser Almeida‐Hernández
- Computational Biochemistry, Center of Medical Biotechnology University of Duisburg‐Essen Essen Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center‐Leibniz Institute for Primate Research Göttingen Germany
- Faculty of Biology and Psychology Georg‐August‐University Göttingen Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center‐Leibniz Institute for Primate Research Göttingen Germany
- Faculty of Biology and Psychology Georg‐August‐University Göttingen Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center‐Leibniz Institute for Primate Research Göttingen Germany
| | - Rishikesh Lotke
- Institute for Medical Virology and Epidemiology of Viral Diseases University Hospital Tübingen Tübingen Germany
| | - Moritz Petersen
- Institute for Medical Virology and Epidemiology of Viral Diseases University Hospital Tübingen Tübingen Germany
| | - Steffen Stenger
- Institute for Microbiology and Hygiene Ulm University Medical Center Ulm Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology Ulm University Medical Center Ulm Germany
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral Diseases University Hospital Tübingen Tübingen Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center‐Leibniz Institute for Primate Research Göttingen Germany
- Faculty of Biology and Psychology Georg‐August‐University Göttingen Germany
| | - Elsa Sanchez‐Garcia
- Computational Biochemistry, Center of Medical Biotechnology University of Duisburg‐Essen Essen Germany
| | - Jan Münch
- Institute of Molecular Virology Ulm University Medical Center Ulm Germany
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Arora P, Kempf A, Nehlmeier I, Schulz SR, Jäck HM, Pöhlmann S, Hoffmann M. Omicron sublineage BQ.1.1 resistance to monoclonal antibodies. Lancet Infect Dis 2023; 23:22-23. [PMID: 36410372 PMCID: PMC9707647 DOI: 10.1016/s1473-3099(22)00733-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/19/2022]
Affiliation(s)
- Prerna Arora
- Infection Biology Unit, German Primate Centre, Leibniz Institute for Primate Research, 37077 Göttingen, Germany,Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Centre, Leibniz Institute for Primate Research, 37077 Göttingen, Germany,Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Centre, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Sebastian R Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Centre, Leibniz Institute for Primate Research, 37077 Göttingen, Germany,Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Centre, Leibniz Institute for Primate Research, 37077 Göttingen, Germany,Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
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Hoffmann M, Behrens GMN, Arora P, Kempf A, Nehlmeier I, Cossmann A, Manthey L, Dopfer-Jablonka A, Pöhlmann S. Effect of hybrid immunity and bivalent booster vaccination on omicron sublineage neutralisation. Lancet Infect Dis 2023; 23:25-28. [PMID: 36480944 PMCID: PMC9721839 DOI: 10.1016/s1473-3099(22)00792-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022]
Affiliation(s)
- Markus Hoffmann
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany.
| | - Georg M N Behrens
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; German Centre for Infection Research, partner site Hannover-Braunschweig, Hannover, Germany; Centre for Individualized Infection Medicine, Hannover, Germany
| | - Prerna Arora
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
| | - Anne Cossmann
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Luis Manthey
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | | | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
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40
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Hoffmann M, Trummer N, Schwartz L, Jankowski J, Lee HK, Willruth LL, Lazareva O, Yuan K, Baumgarten N, Schmidt F, Baumbach J, Schulz MH, Blumenthal DB, Hennighausen L, List M. TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors. Gigascience 2022; 12:giad026. [PMID: 37132521 PMCID: PMC10155229 DOI: 10.1093/gigascience/giad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/23/2023] [Accepted: 04/05/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND Eukaryotic gene expression is controlled by cis-regulatory elements (CREs), including promoters and enhancers, which are bound by transcription factors (TFs). Differential expression of TFs and their binding affinity at putative CREs determine tissue- and developmental-specific transcriptional activity. Consolidating genomic datasets can offer further insights into the accessibility of CREs, TF activity, and, thus, gene regulation. However, the integration and analysis of multimodal datasets are hampered by considerable technical challenges. While methods for highlighting differential TF activity from combined chromatin state data (e.g., chromatin immunoprecipitation [ChIP], ATAC, or DNase sequencing) and RNA sequencing data exist, they do not offer convenient usability, have limited support for large-scale data processing, and provide only minimal functionality for visually interpreting results. RESULTS We developed TF-Prioritizer, an automated pipeline that prioritizes condition-specific TFs from multimodal data and generates an interactive web report. We demonstrated its potential by identifying known TFs along with their target genes, as well as previously unreported TFs active in lactating mouse mammary glands. Additionally, we studied a variety of ENCODE datasets for cell lines K562 and MCF-7, including 12 histone modification ChIP sequencing as well as ATAC and DNase sequencing datasets, where we observe and discuss assay-specific differences. CONCLUSION TF-Prioritizer accepts ATAC, DNase, or ChIP sequencing and RNA sequencing data as input and identifies TFs with differential activity, thus offering an understanding of genome-wide gene regulation, potential pathogenesis, and therapeutic targets in biomedical research.
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Affiliation(s)
- Markus Hoffmann
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising D-85354, Germany
- Institute for Advanced Study, Technical University of Munich, Garching D-85748, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nico Trummer
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising D-85354,Germany
| | - Leon Schwartz
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising D-85354,Germany
| | - Jakub Jankowski
- National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hye Kyung Lee
- National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lina-Liv Willruth
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising D-85354,Germany
| | - Olga Lazareva
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Kevin Yuan
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Nina Baumgarten
- Institute of Cardiovascular Regeneration, Goethe University, 60590 Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590 Frankfurt am Main, Germany
| | - Florian Schmidt
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, 60 Biopolis Street, Singapore138672, Singapore
| | - Jan Baumbach
- Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Computational BioMedicine Lab, University of Southern Denmark, Odense, Denmark
| | - Marcel H Schulz
- Institute of Cardiovascular Regeneration, Goethe University, 60590 Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590 Frankfurt am Main, Germany
| | - David B Blumenthal
- Biomedical Network Science Lab, Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Lothar Hennighausen
- Institute for Advanced Study, Technical University of Munich, Garching D-85748, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Markus List
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising D-85354,Germany
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Heinen N, Marheinecke CS, Bessen C, Blazquez-Navarro A, Roch T, Stervbo U, Anft M, Plaza-Sirvent C, Busse S, Klöhn M, Schrader J, Vidal Blanco E, Urlaub D, Watzl C, Hoffmann M, Pöhlmann S, Tenbusch M, Steinmann E, Todt D, Hagenbeck C, Zimmer G, Schmidt WE, Quast DR, Babel N, Schmitz I, Pfänder S. In-depth analysis of T cell immunity and antibody responses in heterologous prime-boost-boost vaccine regimens against SARS-CoV-2 and Omicron variant. Front Immunol 2022; 13:1062210. [PMID: 36618413 PMCID: PMC9811676 DOI: 10.3389/fimmu.2022.1062210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
With the emergence of novel Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Variants of Concern (VOCs), vaccination studies that elucidate the efficiency and effectiveness of a vaccination campaign are critical to assess the durability and the protective immunity provided by vaccines. SARS-CoV-2 vaccines have been found to induce robust humoral and cell-mediated immunity in individuals vaccinated with homologous vaccination regimens. Recent studies also suggest improved immune response against SARS-CoV-2 when heterologous vaccination strategies are employed. Yet, few data exist on the extent to which heterologous prime-boost-boost vaccinations with two different vaccine platforms have an impact on the T cell-mediated immune responses with a special emphasis on the currently dominantly circulating Omicron strain. In this study, we collected serum and peripheral blood mononuclear cells (PBMCs) from 57 study participants of median 35-year old's working in the health care field, who have received different vaccination regimens. Neutralization assays revealed robust but decreased neutralization of Omicron VOC, including BA.1 and BA.4/5, compared to WT SARS-CoV-2 in all vaccine groups and increased WT SARS-CoV-2 binding and neutralizing antibodies titers in homologous mRNA prime-boost-boost study participants. By investigating cytokine production, we found that homologous and heterologous prime-boost-boost-vaccination induces a robust cytokine response of CD4+ and CD8+ T cells. Collectively, our results indicate robust humoral and T cell mediated immunity against Omicron in homologous and heterologous prime-boost-boost vaccinated study participants, which might serve as a guide for policy decisions.
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Affiliation(s)
- Natalie Heinen
- Department of Molecular & Medical Virology, Ruhr University Bochum, Bochum, Germany
| | | | - Clara Bessen
- Department of Molecular Immunology, Ruhr University Bochum, Bochum, Germany
| | - Arturo Blazquez-Navarro
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital, University Hospital of the Ruhr University Bochum, Herne, Germany,BIH Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin Institute of Health, Berlin, Germany
| | - Toralf Roch
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital, University Hospital of the Ruhr University Bochum, Herne, Germany,BIH Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin Institute of Health, Berlin, Germany
| | - Ulrik Stervbo
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital, University Hospital of the Ruhr University Bochum, Herne, Germany
| | - Moritz Anft
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital, University Hospital of the Ruhr University Bochum, Herne, Germany
| | | | - Sandra Busse
- Department of Molecular Immunology, Ruhr University Bochum, Bochum, Germany
| | - Mara Klöhn
- Department of Molecular & Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Jil Schrader
- Department of Molecular & Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Elena Vidal Blanco
- Department of Molecular & Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Doris Urlaub
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors (IfADo) at TU Dortmund, Dortmund, Germany
| | - Carsten Watzl
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors (IfADo) at TU Dortmund, Dortmund, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
| | - Matthias Tenbusch
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Eike Steinmann
- Department of Molecular & Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Daniel Todt
- Department of Molecular & Medical Virology, Ruhr University Bochum, Bochum, Germany,European Virus Bioinformatics Center, Jena, Germany
| | - Carsten Hagenbeck
- Clinic for Gynecology and Obstetrics, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Gert Zimmer
- Clinic for Gynecology and Obstetrics, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Daniel Robert Quast
- Department of Medicine I, St. Josef-Hospital Bochum, Ruhr University Bochum, Bochum, Germany
| | - Nina Babel
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital, University Hospital of the Ruhr University Bochum, Herne, Germany,BIH Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin Institute of Health, Berlin, Germany
| | - Ingo Schmitz
- Department of Molecular Immunology, Ruhr University Bochum, Bochum, Germany,*Correspondence: Ingo Schmitz, ; Stephanie Pfänder,
| | - Stephanie Pfänder
- Department of Molecular & Medical Virology, Ruhr University Bochum, Bochum, Germany,*Correspondence: Ingo Schmitz, ; Stephanie Pfänder,
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Döller SC, Gutmann T, Hoffmann M, Buntkowsky G. A case study on the influence of hydrophilicity on the signal enhancement by dynamic nuclear polarization. Solid State Nucl Magn Reson 2022; 122:101829. [PMID: 36116176 DOI: 10.1016/j.ssnmr.2022.101829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/25/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
In this work, the behavior of four different commercially available polarizing agents is investigated employing the non-ionic model surfactant 1-octanol as analyte. A relative method for the comparison of the proportion of the direct and indirect polarization transfer pathways is established, allowing a direct comparison of the polarization efficacy for different radicals and different parts of the 1-octanol molecule despite differences in radical concentration or sample amount. With this approach, it could be demonstrated that the hydrophilicity is a key factor in the way polarization is transferred from the polarizing agent to the analyte. These findings are confirmed by the determination of buildup times Tb, illustrating that the choice of polarizing agent plays an essential role in ensuring an optimal polarization transfer and therefore the maximum amount of enhancement possible for DNP enhanced NMR measurements.
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Affiliation(s)
- Sonja C Döller
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, D-64287, Darmstadt, Germany
| | - Torsten Gutmann
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, D-64287, Darmstadt, Germany
| | - Markus Hoffmann
- Department of Chemistry and Biochemistry, State University of New York College at Brockport, Brockport, NY, 14420, USA
| | - Gerd Buntkowsky
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, D-64287, Darmstadt, Germany.
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43
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Arora P, Zhang L, Nehlmeier I, Kempf A, Cossmann A, Dopfer-Jablonka A, Schulz SR, Jäck HM, Behrens GMN, Pöhlmann S, Hoffmann M. The effect of cilgavimab and neutralisation by vaccine-induced antibodies in emerging SARS-CoV-2 BA.4 and BA.5 sublineages. Lancet Infect Dis 2022; 22:1665-1666. [PMID: 36327999 PMCID: PMC9621698 DOI: 10.1016/s1473-3099(22)00693-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Prerna Arora
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Lu Zhang
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Anne Cossmann
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany; Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Alexandra Dopfer-Jablonka
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
| | - Sebastian R Schulz
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany; Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Georg M N Behrens
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany; Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany.
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44
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Leppkes M, Lindemann A, Gößwein S, Paulus S, Roth D, Hartung A, Liebing E, Zundler S, Gonzalez-Acera M, Patankar JV, Mascia F, Scheibe K, Hoffmann M, Uderhardt S, Schauer C, Foersch S, Neufert C, Vieth M, Schett G, Atreya R, Kühl AA, Bleich A, Becker C, Herrmann M, Neurath MF. Neutrophils prevent rectal bleeding in ulcerative colitis by peptidyl-arginine deiminase-4-dependent immunothrombosis. Gut 2022; 71:2414-2429. [PMID: 34862250 PMCID: PMC9667856 DOI: 10.1136/gutjnl-2021-324725] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Bleeding ulcers and erosions are hallmarks of active ulcerative colitis (UC). However, the mechanisms controlling bleeding and mucosal haemostasis remain elusive. DESIGN We used high-resolution endoscopy and colon tissue samples of active UC (n = 36) as well as experimental models of physical and chemical mucosal damage in mice deficient for peptidyl-arginine deiminase-4 (PAD4), gnotobiotic mice and controls. We employed endoscopy, histochemistry, live-cell microscopy and flow cytometry to study eroded mucosal surfaces during mucosal haemostasis. RESULTS Erosions and ulcerations in UC were covered by fresh blood, haematin or fibrin visible by endoscopy. Fibrin layers rather than fresh blood or haematin on erosions were inversely correlated with rectal bleeding in UC. Fibrin layers contained ample amounts of neutrophils coaggregated with neutrophil extracellular traps (NETs) with detectable activity of PAD. Transcriptome analyses showed significantly elevated PAD4 expression in active UC. In experimentally inflicted wounds, we found that neutrophils underwent NET formation in a PAD4-dependent manner hours after formation of primary blood clots, and remodelled clots to immunothrombi containing citrullinated histones, even in the absence of microbiota. PAD4-deficient mice experienced an exacerbated course of dextrane sodium sulfate-induced colitis with markedly increased rectal bleeding (96 % vs 10 %) as compared with controls. PAD4-deficient mice failed to remodel blood clots on mucosal wounds eliciting impaired healing. Thus, NET-associated immunothrombi are protective in acute colitis, while insufficient immunothrombosis is associated with rectal bleeding. CONCLUSION Our findings uncover that neutrophils induce secondary immunothrombosis by PAD4-dependent mechanisms. Insufficient immunothrombosis may favour rectal bleeding in UC.
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Affiliation(s)
- Moritz Leppkes
- Medical Clinic 1, University Clinic, Friedrich Alexander University, Erlangen, Germany .,Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Aylin Lindemann
- Medical Clinic 1, University Clinic, Friedrich Alexander University, Erlangen, Germany
| | - Stefanie Gößwein
- Medical Clinic 1, University Clinic, Friedrich Alexander University, Erlangen, Germany
| | - Susanne Paulus
- Medical Clinic 1, University Clinic, Friedrich Alexander University, Erlangen, Germany
| | - Dominik Roth
- Medical Clinic 1, University Clinic, Friedrich Alexander University, Erlangen, Germany
| | - Anne Hartung
- Medical Clinic 1, University Clinic, Friedrich Alexander University, Erlangen, Germany
| | - Eva Liebing
- Medical Clinic 1, University Clinic, Friedrich Alexander University, Erlangen, Germany
| | - Sebastian Zundler
- Medical Clinic 1, University Clinic, Friedrich Alexander University, Erlangen, Germany,Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Miguel Gonzalez-Acera
- Medical Clinic 1, University Clinic, Friedrich Alexander University, Erlangen, Germany
| | - Jay V Patankar
- Medical Clinic 1, University Clinic, Friedrich Alexander University, Erlangen, Germany
| | - Fabrizio Mascia
- Medical Clinic 1, University Clinic, Friedrich Alexander University, Erlangen, Germany
| | - Kristina Scheibe
- Medical Clinic 1, University Clinic, Friedrich Alexander University, Erlangen, Germany
| | - Markus Hoffmann
- Medical Clinic 3, University Clinic, Friedrich Alexander University, Erlangen, Germany
| | - Stefan Uderhardt
- Deutsches Zentrum Immuntherapie, Erlangen, Germany,Medical Clinic 3, University Clinic, Friedrich Alexander University, Erlangen, Germany
| | - Christine Schauer
- Medical Clinic 3, University Clinic, Friedrich Alexander University, Erlangen, Germany
| | | | - Clemens Neufert
- Medical Clinic 1, University Clinic, Friedrich Alexander University, Erlangen, Germany,Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Michael Vieth
- Friedrich Alexander University, Institute of Pathology, Klinikum Bayreuth, Erlangen, Germany
| | - Georg Schett
- Deutsches Zentrum Immuntherapie, Erlangen, Germany,Medical Clinic 3, University Clinic, Friedrich Alexander University, Erlangen, Germany
| | - Raja Atreya
- Medical Clinic 1, University Clinic, Friedrich Alexander University, Erlangen, Germany,Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Anja A Kühl
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andre Bleich
- Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Christoph Becker
- Medical Clinic 1, University Clinic, Friedrich Alexander University, Erlangen, Germany
| | - Martin Herrmann
- Medical Clinic 3, University Clinic, Friedrich Alexander University, Erlangen, Germany
| | - Markus F Neurath
- Medical Clinic 1, University Clinic, Friedrich Alexander University, Erlangen, Germany,Deutsches Zentrum Immuntherapie, Erlangen, Germany
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Morvan A, Andersen TI, Mi X, Neill C, Petukhov A, Kechedzhi K, Abanin DA, Michailidis A, Acharya R, Arute F, Arya K, Asfaw A, Atalaya J, Bardin JC, Basso J, Bengtsson A, Bortoli G, Bourassa A, Bovaird J, Brill L, Broughton M, Buckley BB, Buell DA, Burger T, Burkett B, Bushnell N, Chen Z, Chiaro B, Collins R, Conner P, Courtney W, Crook AL, Curtin B, Debroy DM, Del Toro Barba A, Demura S, Dunsworth A, Eppens D, Erickson C, Faoro L, Farhi E, Fatemi R, Flores Burgos L, Forati E, Fowler AG, Foxen B, Giang W, Gidney C, Gilboa D, Giustina M, Grajales Dau A, Gross JA, Habegger S, Hamilton MC, Harrigan MP, Harrington SD, Hoffmann M, Hong S, Huang T, Huff A, Huggins WJ, Isakov SV, Iveland J, Jeffrey E, Jiang Z, Jones C, Juhas P, Kafri D, Khattar T, Khezri M, Kieferová M, Kim S, Kitaev AY, Klimov PV, Klots AR, Korotkov AN, Kostritsa F, Kreikebaum JM, Landhuis D, Laptev P, Lau KM, Laws L, Lee J, Lee KW, Lester BJ, Lill AT, Liu W, Locharla A, Malone F, Martin O, McClean JR, McEwen M, Meurer Costa B, Miao KC, Mohseni M, Montazeri S, Mount E, Mruczkiewicz W, Naaman O, Neeley M, Nersisyan A, Newman M, Nguyen A, Nguyen M, Niu MY, O'Brien TE, Olenewa R, Opremcak A, Potter R, Quintana C, Rubin NC, Saei N, Sank D, Sankaragomathi K, Satzinger KJ, Schurkus HF, Schuster C, Shearn MJ, Shorter A, Shvarts V, Skruzny J, Smith WC, Strain D, Sterling G, Su Y, Szalay M, Torres A, Vidal G, Villalonga B, Vollgraff-Heidweiller C, White T, Xing C, Yao Z, Yeh P, Yoo J, Zalcman A, Zhang Y, Zhu N, Neven H, Bacon D, Hilton J, Lucero E, Babbush R, Boixo S, Megrant A, Kelly J, Chen Y, Smelyanskiy V, Aleiner I, Ioffe LB, Roushan P. Formation of robust bound states of interacting microwave photons. Nature 2022; 612:240-245. [PMID: 36477133 PMCID: PMC9729104 DOI: 10.1038/s41586-022-05348-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/14/2022] [Indexed: 12/12/2022]
Abstract
Systems of correlated particles appear in many fields of modern science and represent some of the most intractable computational problems in nature. The computational challenge in these systems arises when interactions become comparable to other energy scales, which makes the state of each particle depend on all other particles1. The lack of general solutions for the three-body problem and acceptable theory for strongly correlated electrons shows that our understanding of correlated systems fades when the particle number or the interaction strength increases. One of the hallmarks of interacting systems is the formation of multiparticle bound states2-9. Here we develop a high-fidelity parameterizable fSim gate and implement the periodic quantum circuit of the spin-½ XXZ model in a ring of 24 superconducting qubits. We study the propagation of these excitations and observe their bound nature for up to five photons. We devise a phase-sensitive method for constructing the few-body spectrum of the bound states and extract their pseudo-charge by introducing a synthetic flux. By introducing interactions between the ring and additional qubits, we observe an unexpected resilience of the bound states to integrability breaking. This finding goes against the idea that bound states in non-integrable systems are unstable when their energies overlap with the continuum spectrum. Our work provides experimental evidence for bound states of interacting photons and discovers their stability beyond the integrability limit.
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Affiliation(s)
- A Morvan
- Google Research, Mountain View, CA, USA
| | | | - X Mi
- Google Research, Mountain View, CA, USA
| | - C Neill
- Google Research, Mountain View, CA, USA
| | | | | | - D A Abanin
- Google Research, Mountain View, CA, USA
- Department of Theoretical Physics, University of Geneva, Geneva, Switzerland
| | - A Michailidis
- Department of Theoretical Physics, University of Geneva, Geneva, Switzerland
| | - R Acharya
- Google Research, Mountain View, CA, USA
| | - F Arute
- Google Research, Mountain View, CA, USA
| | - K Arya
- Google Research, Mountain View, CA, USA
| | - A Asfaw
- Google Research, Mountain View, CA, USA
| | - J Atalaya
- Google Research, Mountain View, CA, USA
| | - J C Bardin
- Google Research, Mountain View, CA, USA
- Department of Electrical and Computer Engineering, University of Massachusetts, Amherst, MA, USA
| | - J Basso
- Google Research, Mountain View, CA, USA
| | | | - G Bortoli
- Google Research, Mountain View, CA, USA
| | | | - J Bovaird
- Google Research, Mountain View, CA, USA
| | - L Brill
- Google Research, Mountain View, CA, USA
| | | | | | - D A Buell
- Google Research, Mountain View, CA, USA
| | - T Burger
- Google Research, Mountain View, CA, USA
| | - B Burkett
- Google Research, Mountain View, CA, USA
| | | | - Z Chen
- Google Research, Mountain View, CA, USA
| | - B Chiaro
- Google Research, Mountain View, CA, USA
| | - R Collins
- Google Research, Mountain View, CA, USA
| | - P Conner
- Google Research, Mountain View, CA, USA
| | | | - A L Crook
- Google Research, Mountain View, CA, USA
| | - B Curtin
- Google Research, Mountain View, CA, USA
| | | | | | - S Demura
- Google Research, Mountain View, CA, USA
| | | | - D Eppens
- Google Research, Mountain View, CA, USA
| | | | - L Faoro
- Google Research, Mountain View, CA, USA
| | - E Farhi
- Google Research, Mountain View, CA, USA
| | - R Fatemi
- Google Research, Mountain View, CA, USA
| | | | - E Forati
- Google Research, Mountain View, CA, USA
| | | | - B Foxen
- Google Research, Mountain View, CA, USA
| | - W Giang
- Google Research, Mountain View, CA, USA
| | - C Gidney
- Google Research, Mountain View, CA, USA
| | - D Gilboa
- Google Research, Mountain View, CA, USA
| | | | | | - J A Gross
- Google Research, Mountain View, CA, USA
| | | | | | | | | | | | - S Hong
- Google Research, Mountain View, CA, USA
| | - T Huang
- Google Research, Mountain View, CA, USA
| | - A Huff
- Google Research, Mountain View, CA, USA
| | | | | | - J Iveland
- Google Research, Mountain View, CA, USA
| | - E Jeffrey
- Google Research, Mountain View, CA, USA
| | - Z Jiang
- Google Research, Mountain View, CA, USA
| | - C Jones
- Google Research, Mountain View, CA, USA
| | - P Juhas
- Google Research, Mountain View, CA, USA
| | - D Kafri
- Google Research, Mountain View, CA, USA
| | - T Khattar
- Google Research, Mountain View, CA, USA
| | - M Khezri
- Google Research, Mountain View, CA, USA
| | - M Kieferová
- Google Research, Mountain View, CA, USA
- Centre for Quantum Computation and Communication Technology, Centre for Quantum Software and Information, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - S Kim
- Google Research, Mountain View, CA, USA
| | - A Y Kitaev
- Google Research, Mountain View, CA, USA
- Institute for Quantum Information and Matter, California Institute of Technology, Pasadena, CA, USA
| | | | - A R Klots
- Google Research, Mountain View, CA, USA
| | - A N Korotkov
- Google Research, Mountain View, CA, USA
- Department of Electrical and Computer Engineering, University of California, Riverside, CA, USA
| | | | | | | | - P Laptev
- Google Research, Mountain View, CA, USA
| | - K-M Lau
- Google Research, Mountain View, CA, USA
| | - L Laws
- Google Research, Mountain View, CA, USA
| | - J Lee
- Google Research, Mountain View, CA, USA
| | - K W Lee
- Google Research, Mountain View, CA, USA
| | | | - A T Lill
- Google Research, Mountain View, CA, USA
| | - W Liu
- Google Research, Mountain View, CA, USA
| | | | - F Malone
- Google Research, Mountain View, CA, USA
| | - O Martin
- Google Research, Mountain View, CA, USA
| | | | - M McEwen
- Google Research, Mountain View, CA, USA
- Department of Physics, University of California, Santa Barbara, CA, USA
| | | | - K C Miao
- Google Research, Mountain View, CA, USA
| | - M Mohseni
- Google Research, Mountain View, CA, USA
| | | | - E Mount
- Google Research, Mountain View, CA, USA
| | | | - O Naaman
- Google Research, Mountain View, CA, USA
| | - M Neeley
- Google Research, Mountain View, CA, USA
| | | | - M Newman
- Google Research, Mountain View, CA, USA
| | - A Nguyen
- Google Research, Mountain View, CA, USA
| | - M Nguyen
- Google Research, Mountain View, CA, USA
| | - M Y Niu
- Google Research, Mountain View, CA, USA
| | | | - R Olenewa
- Google Research, Mountain View, CA, USA
| | | | - R Potter
- Google Research, Mountain View, CA, USA
| | | | - N C Rubin
- Google Research, Mountain View, CA, USA
| | - N Saei
- Google Research, Mountain View, CA, USA
| | - D Sank
- Google Research, Mountain View, CA, USA
| | | | | | | | | | | | - A Shorter
- Google Research, Mountain View, CA, USA
| | - V Shvarts
- Google Research, Mountain View, CA, USA
| | - J Skruzny
- Google Research, Mountain View, CA, USA
| | - W C Smith
- Google Research, Mountain View, CA, USA
| | - D Strain
- Google Research, Mountain View, CA, USA
| | | | - Y Su
- Google Research, Mountain View, CA, USA
| | - M Szalay
- Google Research, Mountain View, CA, USA
| | - A Torres
- Google Research, Mountain View, CA, USA
| | - G Vidal
- Google Research, Mountain View, CA, USA
| | | | | | - T White
- Google Research, Mountain View, CA, USA
| | - C Xing
- Google Research, Mountain View, CA, USA
| | - Z Yao
- Google Research, Mountain View, CA, USA
| | - P Yeh
- Google Research, Mountain View, CA, USA
| | - J Yoo
- Google Research, Mountain View, CA, USA
| | - A Zalcman
- Google Research, Mountain View, CA, USA
| | - Y Zhang
- Google Research, Mountain View, CA, USA
| | - N Zhu
- Google Research, Mountain View, CA, USA
| | - H Neven
- Google Research, Mountain View, CA, USA
| | - D Bacon
- Google Research, Mountain View, CA, USA
| | - J Hilton
- Google Research, Mountain View, CA, USA
| | - E Lucero
- Google Research, Mountain View, CA, USA
| | - R Babbush
- Google Research, Mountain View, CA, USA
| | - S Boixo
- Google Research, Mountain View, CA, USA
| | - A Megrant
- Google Research, Mountain View, CA, USA
| | - J Kelly
- Google Research, Mountain View, CA, USA
| | - Y Chen
- Google Research, Mountain View, CA, USA
| | | | - I Aleiner
- Google Research, Mountain View, CA, USA.
| | - L B Ioffe
- Google Research, Mountain View, CA, USA.
| | - P Roushan
- Google Research, Mountain View, CA, USA.
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Korenblik R, van Zon JFJA, Olij B, Heil J, Dewulf MJL, Neumann UP, Olde Damink SWM, Binkert CA, Schadde E, van der Leij C, van Dam RM, van Baardewijk LJ, Barbier L, Binkert CA, Billingsley K, Björnsson B, Andorrà EC, Arslan B, Baclija I, Bemelmans MHA, Bent C, de Boer MT, Bokkers RPH, de Boo DW, Breen D, Breitenstein S, Bruners P, Cappelli A, Carling U, Robert MCI, Chan B, De Cobelli F, Choi J, Crawford M, Croagh D, van Dam RM, Deprez F, Detry O, Dewulf MJL, Díaz-Nieto R, Dili A, Erdmann JI, Font JC, Davis R, Delle M, Fernando R, Fisher O, Fouraschen SMG, Fretland ÅA, Fundora Y, Gelabert A, Gerard L, Gobardhan P, Gómez F, Guiliante F, Grünberger T, Grochola LF, Grünhagen DJ, Guitart J, Hagendoorn J, Heil J, Heise D, Herrero E, Hess G, Hilal MA, Hoffmann M, Iezzi R, Imani F, Inmutto N, James S, Borobia FJG, Jovine E, Kalil J, Kingham P, Kollmar O, Kleeff J, van der Leij C, Lopez-Ben S, Macdonald A, Meijerink M, Korenblik R, Lapisatepun W, Leclercq WKG, Lindsay R, Lucidi V, Madoff DC, Martel G, Mehrzad H, Menon K, Metrakos P, Modi S, Moelker A, Montanari N, Moragues JS, Navinés-López J, Neumann UP, Nguyen J, Peddu P, Primrose JN, Olde Damink SWM, Qu X, Raptis DA, Ratti F, Ryan S, Ridouani F, Rinkes IHMB, Rogan C, Ronellenfitsch U, Serenari M, Salik A, Sallemi C, Sandström P, Martin ES, Sarría L, Schadde E, Serrablo A, Settmacher U, Smits J, Smits MLJ, Snitzbauer A, Soonawalla Z, Sparrelid E, Spuentrup E, Stavrou GA, Sutcliffe R, Tancredi I, Tasse JC, Teichgräber U, Udupa V, Valenti DA, Vass D, Vogl TJ, Wang X, White S, De Wispelaere JF, Wohlgemuth WA, Yu D, Zijlstra IJAJ. Resectability of bilobar liver tumours after simultaneous portal and hepatic vein embolization versus portal vein embolization alone: meta-analysis. BJS Open 2022; 6:6844022. [PMID: 36437731 PMCID: PMC9702575 DOI: 10.1093/bjsopen/zrac141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/09/2022] [Accepted: 10/05/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Many patients with bi-lobar liver tumours are not eligible for liver resection due to an insufficient future liver remnant (FLR). To reduce the risk of posthepatectomy liver failure and the primary cause of death, regenerative procedures intent to increase the FLR before surgery. The aim of this systematic review is to provide an overview of the available literature and outcomes on the effectiveness of simultaneous portal and hepatic vein embolization (PVE/HVE) versus portal vein embolization (PVE) alone. METHODS A systematic literature search was conducted in PubMed, Web of Science, and Embase up to September 2022. The primary outcome was resectability and the secondary outcome was the FLR volume increase. RESULTS Eight studies comparing PVE/HVE with PVE and six retrospective PVE/HVE case series were included. Pooled resectability within the comparative studies was 75 per cent in the PVE group (n = 252) versus 87 per cent in the PVE/HVE group (n = 166, OR 1.92 (95% c.i., 1.13-3.25)) favouring PVE/HVE (P = 0.015). After PVE, FLR hypertrophy between 12 per cent and 48 per cent (after a median of 21-30 days) was observed, whereas growth between 36 per cent and 67 per cent was reported after PVE/HVE (after a median of 17-31 days). In the comparative studies, 90-day primary cause of death was similar between groups (2.5 per cent after PVE versus 2.2 per cent after PVE/HVE), but a higher 90-day primary cause of death was reported in single-arm PVE/HVE cohort studies (6.9 per cent, 12 of 175 patients). CONCLUSION Based on moderate/weak evidence, PVE/HVE seems to increase resectability of bi-lobar liver tumours with a comparable safety profile. Additionally, PVE/HVE resulted in faster and more pronounced hypertrophy compared with PVE alone.
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Affiliation(s)
- Remon Korenblik
- Correspondence to: R. K., Universiteigssingel 50 (room 5.452) 6229 ER Maastricht, The Netherlands (e-mail: ); R. M. v. D., Maastricht UMC+, Dept. of Surgery, Level 4, PO Box 5800, 6202 AZ Maastricht, The Netherlands (e-mail: )
| | - Jasper F J A van Zon
- Department of Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Bram Olij
- Department of Surgery, Maastricht University Medical Center, Maastricht, The Netherlands,GROW—Department of Surgery, School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands,Department of General, Visceral and Transplant Surgery, University Hospital RWTH Aachen, Aachen, Germany
| | - Jan Heil
- Department of General, Visceral and Transplant Surgery, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maxime J L Dewulf
- Department of Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ulf P Neumann
- Department of Surgery, Maastricht University Medical Center, Maastricht, The Netherlands,Department of General, Visceral and Transplant Surgery, University Hospital RWTH Aachen, Aachen, Germany
| | - Steven W M Olde Damink
- Department of Surgery, Maastricht University Medical Center, Maastricht, The Netherlands,Department of General, Visceral and Transplant Surgery, University Hospital RWTH Aachen, Aachen, Germany,NUTRIM—Department of Surgery, School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Christoph A Binkert
- Department of Radiology, Cantonal Hospital Winterthur, Winterthur, Switzerland
| | - Erik Schadde
- Department of General, Visceral and Transplant Surgery, Klinik Hirslanden, Zurich, Switzerland,Department of General, Visceral and Transplant Surgery, Hirslanden Klink St. Anna Luzern, Luzern, Switzerland
| | | | - Ronald M van Dam
- Correspondence to: R. K., Universiteigssingel 50 (room 5.452) 6229 ER Maastricht, The Netherlands (e-mail: ); R. M. v. D., Maastricht UMC+, Dept. of Surgery, Level 4, PO Box 5800, 6202 AZ Maastricht, The Netherlands (e-mail: )
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Hamusonde K, Nicca D, Günthard HF, Stöckle M, Darling KEA, Calmy A, Bernasconi E, Haerry D, Schmid P, Kouyos RD, Rauch A, Salazar-Vizcaya L, Aebi-Popp K, Anagnostopoulos A, Battegay M, Bernasconi E, Braun DL, Bucher HC, Calmy A, Cavassini M, Ciuffi A, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Günthard HF, Hachfeld A, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Huber M, Jackson-Perry D, Kahlert CR, Kaiser L, Keiser O, Klimkait T, Kouyos RD, Kovari H, Kusejko K, Labhardt N, Leuzinger K, Martinez de Tejada B, Marzolini C, Metzner KJ, Müller N, Nemeth J, Nicca D, Notter J, Paioni P, Pantaleo G, Perreau M, Rauch A, Salazar-Vizcaya L, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Wandeler G, Weisser M, Yerly S. Triggers of Change in Sexual Behavior Among People With HIV: The Swiss U U Statement and COVID-19 Compared. J Infect Dis 2022; 227:407-411. [PMID: 36408629 PMCID: PMC9891402 DOI: 10.1093/infdis/jiac459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
We assessed changes in sexual behavior among people with human immunodeficiency virus (HIV) over 20 years. Condom use with stable partners steadily declined from over 90 to 29 since the Swiss U U statement, with similar trajectories between men who have sex with men (MSM) and heterosexuals. Occasional partnership remained higher among MSM compared to heterosexuals even during coronavirus disease 2019 (COVID-19) social distancing.
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Affiliation(s)
- Kalongo Hamusonde
- Correspondence: K. Hamusonde, Msc, Bern University Hospital, Inselspital, Universitätsklinik für Infektiologie, Personalhaus 6, Bern 3010, Switzerland ()
| | - Dunja Nicca
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Marcel Stöckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Katharine E A Darling
- Service of Infectious Diseases, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Alexandra Calmy
- Division of Infectious Diseases, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Ente Ospedaliero Cantonale, University of Southern Switzerland, Lugano, Switzerland
| | | | - Patrick Schmid
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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48
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Jacobsen H, Strengert M, Maaß H, Ynga Durand MA, Katzmarzyk M, Kessel B, Harries M, Rand U, Abassi L, Kim Y, Lüddecke T, Metzdorf K, Hernandez P, Ortmann J, Heise JK, Castell S, Gornyk D, Glöckner S, Melhorn V, Kemmling Y, Lange B, Dulovic A, Marsall P, Häring J, Junker D, Schneiderhan-Marra N, Hoffmann M, Pöhlmann S, Krause G, Cicin-Sain L. Diminished neutralization responses towards SARS-CoV-2 Omicron VoC after mRNA or vector-based COVID-19 vaccinations. Sci Rep 2022; 12:19858. [PMID: 36400804 PMCID: PMC9673895 DOI: 10.1038/s41598-022-22552-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 10/17/2022] [Indexed: 11/19/2022] Open
Abstract
SARS-CoV-2 variants accumulating immune escape mutations provide a significant risk to vaccine-induced protection against infection. The novel variant of concern (VoC) Omicron BA.1 and its sub-lineages have the largest number of amino acid alterations in its Spike protein to date. Thus, they may efficiently escape recognition by neutralizing antibodies, allowing breakthrough infections in convalescent and vaccinated individuals in particular in those who have only received a primary immunization scheme. We analyzed neutralization activity of sera from individuals after vaccination with all mRNA-, vector- or heterologous immunization schemes currently available in Europe by in vitro neutralization assay at peak response towards SARS-CoV-2 B.1, Omicron sub-lineages BA.1, BA.2, BA.2.12.1, BA.3, BA.4/5, Beta and Delta pseudotypes and also provide longitudinal follow-up data from BNT162b2 vaccinees. All vaccines apart from Ad26.CoV2.S showed high levels of responder rates (96-100%) towards the SARS-CoV-2 B.1 isolate, and minor to moderate reductions in neutralizing Beta and Delta VoC pseudotypes. The novel Omicron variant and its sub-lineages had the biggest impact, both in terms of response rates and neutralization titers. Only mRNA-1273 showed a 100% response rate to Omicron BA.1 and induced the highest level of neutralizing antibody titers, followed by heterologous prime-boost approaches. Homologous BNT162b2 vaccination, vector-based AZD1222 and Ad26.CoV2.S performed less well with peak responder rates of 48%, 56% and 9%, respectively. However, Omicron responder rates in BNT162b2 recipients were maintained in our six month longitudinal follow-up indicating that individuals with cross-protection against Omicron maintain it over time. Overall, our data strongly argue for booster doses in individuals who were previously vaccinated with BNT162b2, or a vector-based primary immunization scheme.
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Affiliation(s)
- Henning Jacobsen
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Monika Strengert
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, Joint Venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Henrike Maaß
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Maeva Katzmarzyk
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Barbora Kessel
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Manuela Harries
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ulfert Rand
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Leila Abassi
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Yeonsu Kim
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Tatjana Lüddecke
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Kristin Metzdorf
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Pilar Hernandez
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Julia Ortmann
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jana-Kristin Heise
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefanie Castell
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Daniela Gornyk
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stephan Glöckner
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Vanessa Melhorn
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Yvonne Kemmling
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Berit Lange
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Alex Dulovic
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Patrick Marsall
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Julia Häring
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Daniel Junker
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | | | - Markus Hoffmann
- Deutsches Primatenzentrum, Leibniz-Institut Für Primatenforschung, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University, Göttingen, Germany
| | - Stefan Pöhlmann
- Deutsches Primatenzentrum, Leibniz-Institut Für Primatenforschung, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University, Göttingen, Germany
| | - Gérard Krause
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
- TWINCORE, Centre for Experimental and Clinical Infection Research, Joint Venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany.
| | - Luka Cicin-Sain
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany.
- Centre for Individualized Infection Medicine (CIIM), Joint Venture of Helmholtz Centre for Infection Research and Medical School Hannover, Inhoffenstraße 7, 38124, Braunschweig, Germany.
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49
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Mi X, Sonner M, Niu MY, Lee KW, Foxen B, Acharya R, Aleiner I, Andersen TI, Arute F, Arya K, Asfaw A, Atalaya J, Bardin JC, Basso J, Bengtsson A, Bortoli G, Bourassa A, Brill L, Broughton M, Buckley BB, Buell DA, Burkett B, Bushnell N, Chen Z, Chiaro B, Collins R, Conner P, Courtney W, Crook AL, Debroy DM, Demura S, Dunsworth A, Eppens D, Erickson C, Faoro L, Farhi E, Fatemi R, Flores L, Forati E, Fowler AG, Giang W, Gidney C, Gilboa D, Giustina M, Dau AG, Gross JA, Habegger S, Harrigan MP, Hoffmann M, Hong S, Huang T, Huff A, Huggins WJ, Ioffe LB, Isakov SV, Iveland J, Jeffrey E, Jiang Z, Jones C, Kafri D, Kechedzhi K, Khattar T, Kim S, Kitaev AY, Klimov PV, Klots AR, Korotkov AN, Kostritsa F, Kreikebaum JM, Landhuis D, Laptev P, Lau KM, Lee J, Laws L, Liu W, Locharla A, Martin O, McClean JR, McEwen M, Meurer Costa B, Miao KC, Mohseni M, Montazeri S, Morvan A, Mount E, Mruczkiewicz W, Naaman O, Neeley M, Neill C, Newman M, O’Brien TE, Opremcak A, Petukhov A, Potter R, Quintana C, Rubin NC, Saei N, Sank D, Sankaragomathi K, Satzinger KJ, Schuster C, Shearn MJ, Shvarts V, Strain D, Su Y, Szalay M, Vidal G, Villalonga B, Vollgraff-Heidweiller C, White T, Yao Z, Yeh P, Yoo J, Zalcman A, Zhang Y, Zhu N, Neven H, Bacon D, Hilton J, Lucero E, Babbush R, Boixo S, Megrant A, Chen Y, Kelly J, Smelyanskiy V, Abanin DA, Roushan P. Noise-resilient edge modes on a chain of superconducting qubits. Science 2022; 378:785-790. [DOI: 10.1126/science.abq5769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Inherent symmetry of a quantum system may protect its otherwise fragile states. Leveraging such protection requires testing its robustness against uncontrolled environmental interactions. Using 47 superconducting qubits, we implement the one-dimensional kicked Ising model, which exhibits nonlocal Majorana edge modes (MEMs) with
ℤ
2
parity symmetry. We find that any multiqubit Pauli operator overlapping with the MEMs exhibits a uniform late-time decay rate comparable to single-qubit relaxation rates, irrespective of its size or composition. This characteristic allows us to accurately reconstruct the exponentially localized spatial profiles of the MEMs. Furthermore, the MEMs are found to be resilient against certain symmetry-breaking noise owing to a prethermalization mechanism. Our work elucidates the complex interplay between noise and symmetry-protected edge modes in a solid-state environment.
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Affiliation(s)
- X. Mi
- Google Research, Mountain View, CA, USA
| | - M. Sonner
- Department of Theoretical Physics, University of Geneva, Geneva, Switzerland
| | - M. Y. Niu
- Google Research, Mountain View, CA, USA
| | - K. W. Lee
- Google Research, Mountain View, CA, USA
| | - B. Foxen
- Google Research, Mountain View, CA, USA
| | | | | | | | - F. Arute
- Google Research, Mountain View, CA, USA
| | - K. Arya
- Google Research, Mountain View, CA, USA
| | - A. Asfaw
- Google Research, Mountain View, CA, USA
| | | | - J. C. Bardin
- Google Research, Mountain View, CA, USA
- Department of Electrical and Computer Engineering, University of Massachusetts, Amherst, MA, USA
| | - J. Basso
- Google Research, Mountain View, CA, USA
| | | | | | | | - L. Brill
- Google Research, Mountain View, CA, USA
| | | | | | | | | | | | - Z. Chen
- Google Research, Mountain View, CA, USA
| | - B. Chiaro
- Google Research, Mountain View, CA, USA
| | | | - P. Conner
- Google Research, Mountain View, CA, USA
| | | | | | | | - S. Demura
- Google Research, Mountain View, CA, USA
| | | | - D. Eppens
- Google Research, Mountain View, CA, USA
| | | | - L. Faoro
- Google Research, Mountain View, CA, USA
| | - E. Farhi
- Google Research, Mountain View, CA, USA
| | - R. Fatemi
- Google Research, Mountain View, CA, USA
| | - L. Flores
- Google Research, Mountain View, CA, USA
| | - E. Forati
- Google Research, Mountain View, CA, USA
| | | | - W. Giang
- Google Research, Mountain View, CA, USA
| | - C. Gidney
- Google Research, Mountain View, CA, USA
| | - D. Gilboa
- Google Research, Mountain View, CA, USA
| | | | - A. G. Dau
- Google Research, Mountain View, CA, USA
| | | | | | | | | | - S. Hong
- Google Research, Mountain View, CA, USA
| | - T. Huang
- Google Research, Mountain View, CA, USA
| | - A. Huff
- Google Research, Mountain View, CA, USA
| | | | | | | | | | | | - Z. Jiang
- Google Research, Mountain View, CA, USA
| | - C. Jones
- Google Research, Mountain View, CA, USA
| | - D. Kafri
- Google Research, Mountain View, CA, USA
| | | | | | - S. Kim
- Google Research, Mountain View, CA, USA
| | - A. Y. Kitaev
- Google Research, Mountain View, CA, USA
- Institute for Quantum Information and Matter, California Institute of Technology, Pasadena, CA, USA
| | | | | | - A. N. Korotkov
- Google Research, Mountain View, CA, USA
- Department of Electrical and Computer Engineering, University of California, Riverside, CA, USA
| | | | | | | | - P. Laptev
- Google Research, Mountain View, CA, USA
| | - K.-M. Lau
- Google Research, Mountain View, CA, USA
| | - J. Lee
- Google Research, Mountain View, CA, USA
| | - L. Laws
- Google Research, Mountain View, CA, USA
| | - W. Liu
- Google Research, Mountain View, CA, USA
| | | | - O. Martin
- Google Research, Mountain View, CA, USA
| | | | - M. McEwen
- Google Research, Mountain View, CA, USA
- Department of Physics, University of California, Santa Barbara, CA, USA
| | | | | | | | | | - A. Morvan
- Google Research, Mountain View, CA, USA
| | - E. Mount
- Google Research, Mountain View, CA, USA
| | | | - O. Naaman
- Google Research, Mountain View, CA, USA
| | - M. Neeley
- Google Research, Mountain View, CA, USA
| | - C. Neill
- Google Research, Mountain View, CA, USA
| | - M. Newman
- Google Research, Mountain View, CA, USA
| | | | | | | | - R. Potter
- Google Research, Mountain View, CA, USA
| | | | | | - N. Saei
- Google Research, Mountain View, CA, USA
| | - D. Sank
- Google Research, Mountain View, CA, USA
| | | | | | | | | | | | - D. Strain
- Google Research, Mountain View, CA, USA
| | - Y. Su
- Google Research, Mountain View, CA, USA
| | - M. Szalay
- Google Research, Mountain View, CA, USA
| | - G. Vidal
- Google Research, Mountain View, CA, USA
| | | | | | - T. White
- Google Research, Mountain View, CA, USA
| | - Z. Yao
- Google Research, Mountain View, CA, USA
| | - P. Yeh
- Google Research, Mountain View, CA, USA
| | - J. Yoo
- Google Research, Mountain View, CA, USA
| | | | - Y. Zhang
- Google Research, Mountain View, CA, USA
| | - N. Zhu
- Google Research, Mountain View, CA, USA
| | - H. Neven
- Google Research, Mountain View, CA, USA
| | - D. Bacon
- Google Research, Mountain View, CA, USA
| | - J. Hilton
- Google Research, Mountain View, CA, USA
| | - E. Lucero
- Google Research, Mountain View, CA, USA
| | | | - S. Boixo
- Google Research, Mountain View, CA, USA
| | | | - Y. Chen
- Google Research, Mountain View, CA, USA
| | - J. Kelly
- Google Research, Mountain View, CA, USA
| | | | - D. A. Abanin
- Google Research, Mountain View, CA, USA
- Department of Theoretical Physics, University of Geneva, Geneva, Switzerland
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50
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Bosetti D, Mugglin C, Calmy A, Cavassini M, Stöckle M, Braun D, Notter J, Haerry D, Hampel B, Kovari H, Bernasconi E, Wandeler G, Rauch A, Aebi-Popp K, Anagnostopoulos A, Battegay M, Bernasconi E, Braun DL, Bucher HC, Calmy A, Cavassini M, Ciuffi A, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Günthard HF, Hachfeld A, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Huber M, Kahlert CR, Kaiser L, Keiser O, Klimkait T, Kouyos RD, Kovari H, Kusejko K, Martinetti G, Martinez de Tejada B, Marzolini C, Metzner KJ, Müller N, Nemeth J, Nicca D, Paioni P, Pantaleo G, Perreau M, Rauch A, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Wandeler G, Yerly S. Risk Factors and Incidence of Sexually Transmitted Infections in the Swiss HIV Cohort Study. Open Forum Infect Dis 2022; 9:ofac592. [PMID: 36504700 PMCID: PMC9728517 DOI: 10.1093/ofid/ofac592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/15/2022] [Indexed: 11/17/2022] Open
Abstract
Background Sexually transmitted infections (STIs) are common among people with human immunodeficiency virus (PWH), but there are limited data about risk factors and incidence of STIs in large, representative cohort studies. Methods We assessed incidence and risk factors of STIs reported by treating physicians within the Swiss HIV Cohort Study (SHCS). Sexually transmitted infections and demographic, clinical, and behavioral characteristics were prospectively collected at 6-month follow-up visits between October 2017 and November 2019. We used multilevel Poisson regression to assess incidence rate ratios of different STIs. Results Among 10 140 study participants, a total of 1634 STIs in 1029 SHCS participants were reported over 17 766 person-years of follow up (PYFUP). The overall incidence of any reported STI was 91.9 per 1000 PYFU (95% confidence interval [CI], 85.8 -98.5). Among the 1634 STI episodes, there were 573 (35.1%) incident cases of syphilis, 497 gonorrhea (30.4%), and 418 chlamydia (25.6%). Men who have sex with men (MSM) younger than 50 years represented 21% of the study population, but accounted for 61% of reported STIs. Male sex (adjusted incidence rate ratio [aIRR], 2.03; 95% CI, 1.36-3.02), MSM (aIRR, 3.62; 95% CI, 2.88-4.55), age group 18-34 years (aIRR, 1.78; 95% CI, 1.51-2.10), history of sexual relationships with occasional partners (aIRR, 6.87; 95% CI, 5.40-8.73), and reporting injecting drug use (aIRR, 2.48; 95% CI, 1.91-3.23) were associated with a higher risk of incident STIs. Conclusions Sexually transmitted infections were frequent among PWH and varied considerably between age and risk groups. Screening programs and recommendations for STI testing need to be adapted according to risk factors and demographic characteristics.
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Affiliation(s)
| | - Catrina Mugglin
- Correspondence: Catrina Mugglin, MSc, MD, PhD, Inselspital, Bern University Hospital, Freiburgstrasse, CH-3010 Bern, Switzerland ()
| | - Alexandra Calmy
- HIV/AIDS Unit, Department of Infectious Diseases, Geneva, Switzerland
| | - Matthias Cavassini
- University Hospital of Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Marcel Stöckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Dominique Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Julia Notter
- Division of Infectious Diseases and Hospital Epidemiology, St. Gallen, Switzerland
| | | | - Benjamin Hampel
- Department of Public and Global Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland,Checkpoint Zurich, Zurich, Switzerland
| | - Helen Kovari
- Zentrum für Infektionskrankheiten, Klinik im Park, Zurich, Switzerland
| | - Enos Bernasconi
- Ente Ospedaliero Cantonale, Lugano, University of Geneva, and University of Southern Switzerland, Lugano, Switzerland
| | - Gilles Wandeler
- Department of Infectious Diseases, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
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