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Castelletti N, Paunovic I, Rubio-Acero R, Beyerl J, Plank M, Reinkemeyer C, Kroidl I, Noreña I, Winter S, Olbrich L, Janke C, Hoelscher M, Wieser A. A Dried Blood Spot protocol for high-throughput quantitative analysis of SARS-CoV-2 RBD serology based on the Roche Elecsys system. Microbiol Spectr 2024; 12:e0288523. [PMID: 38426747 DOI: 10.1128/spectrum.02885-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/15/2023] [Indexed: 03/02/2024] Open
Abstract
SARS-CoV-2 spreads pandemically since 2020; in 2021, effective vaccinations became available and vaccination campaigns commenced. Still, it is hard to track the spread of the infection or to assess vaccination success in the broader population. Measuring specific anti-SARS-CoV-2 antibodies is the most effective tool to track the spread of the infection or successful vaccinations. The need for venous-blood sampling however poses a significant barrier for large studies. Dried-blood-spots on filter-cards (DBS) have been used for SARS-CoV-2 serology in our laboratory, but so far not to follow quantitative SARS-CoV-2 anti-spike reactivity in a longitudinal cohort. We developed a semi-automated protocol or quantitative SARS-CoV-2 anti-spike serology from self-sampled DBS, validating it in a cohort of matched DBS and venous-blood samples (n = 825). We investigated chromatographic effects, reproducibility, and carry-over effects and calculated a positivity threshold as well as a conversion formula to determine the quantitative binding units in the DBS with confidence intervals. Sensitivity and specificity reached 96.63% and 97.81%, respectively, compared to the same test performed in paired venous samples. Between a signal of 0.018 and 250 U/mL, we calculated a correction formula. Measuring longitudinal samples during vaccinations, we demonstrated relative changes in titers over time in several individuals and in a longitudinal cohort over four follow-ups. DBS sampling has proven itself for anti-nucleocapsid serosurveys in our laboratory. Similarly, anti-spike high-throughput DBS serology is feasible as a complementary assay. Quantitative measurements are accurate enough to follow titer dynamics in populations also after vaccination campaigns. This work was supported by the Bavarian State Ministry of Science and the Arts; LMU University Hospital, LMU Munich; Helmholtz Center Munich; University of Bonn; University of Bielefeld; German Ministry for Education and Research (proj. nr.: 01KI20271 and others) and the Medical Biodefense Research Program of the Bundeswehr Medical Service. Roche Diagnostics provided kits and machines for analyses at discounted rates. The project is funded also by the European-wide Consortium ORCHESTRA. The ORCHESTRA project has received funding from the European Union's Horizon 2020 research and innovation program under grant agreement No 101016167. The views expressed in this publication are the sole responsibility of the author, and the Commission is not responsible for any use that may be made of the information it contains.IMPORTANCESARS-CoV-2 has been spreading globally as a pandemic since 2020. To determine the prevalence of SARS-CoV-2 antibodies among populations, the most effective public health tool is measuring specific anti-SARS-CoV-2 antibodies induced by infection or vaccination. However, conducting large-scale studies that involve venous-blood sampling is challenging due to the associated feasibility and cost issues. A more cost-efficient and less invasive method for SARS-CoV-2 serological testing is using Dried-Blood-Spots on filter cards (DBS). In this paper, we have developed a semi-automated protocol for quantifying SARS-CoV-2 anti-spike antibodies from self-collected DBS. Our laboratory has previously successfully used DBS sampling for anti-nucleocapsid antibody surveys. Likewise, conducting high-throughput DBS serology for anti-spike antibodies is feasible as an additional test that can be performed using the same sample preparation as the anti-nucleocapsid analysis. The quantitative measurements obtained are accurate enough to track the dynamics of antibody levels in populations, even after vaccination campaigns.
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Affiliation(s)
- Noemi Castelletti
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
- Institute of Radiation Medicine, Helmholtz Zentrum München, Neuherberg, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, Munich, Germany
| | - Ivana Paunovic
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, Munich, Germany
- Max-von-Pettenkofer Institute, LMU Munich, Munich, Germany
| | - Raquel Rubio-Acero
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
| | - Jessica Beyerl
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, Munich, Germany
- Max-von-Pettenkofer Institute, LMU Munich, Munich, Germany
| | - Michael Plank
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
| | - Christina Reinkemeyer
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
| | - Inge Kroidl
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Ivan Noreña
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
| | - Simon Winter
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, Munich, Germany
| | - Laura Olbrich
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Christian Janke
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
- Center for International Health (CIH), University Hospital, LMU Munich, Munich, Germany
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, Munich, Germany
- Max-von-Pettenkofer Institute, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
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Plank M, Carmiol N, Mitri B, Lipinski AA, Langlais PR, Capaldi AP. Systems level analysis of time and stimuli specific signaling through PKA. Mol Biol Cell 2024; 35:ar60. [PMID: 38446618 DOI: 10.1091/mbc.e23-02-0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024] Open
Abstract
It is well known that eukaryotic cells create gradients of cAMP across space and time to regulate the cAMP dependent protein kinase (PKA) and, in turn, growth and metabolism. However, it is unclear how PKA responds to different concentrations of cAMP. Here, to address this question, we examine PKA signaling in Saccharomyces cerevisiae in different conditions, timepoints, and concentrations of the chemical inhibitor 1-NM-PP1, using phosphoproteomics. These experiments show that there are numerous proteins that are only phosphorylated when cAMP and PKA activity are at/near their maximum level, while other proteins are phosphorylated even when cAMP levels and PKA activity are low. The data also show that PKA drives cells into distinct growth states by acting on proteins with different thresholds for phosphorylation in different conditions. Analysis of the sequences surrounding the 118 PKA-dependent phosphosites suggests that the phosphorylation thresholds are set, at least in part, by the affinity of PKA for each site.
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Affiliation(s)
- Michael Plank
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
- The Bio5 Institute, University of Arizona, Tucson, AZ 85721
| | - Nicole Carmiol
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
| | - Bassam Mitri
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
| | | | - Paul R Langlais
- The Department of Medicine, University of Arizona, Tucson, AZ 85721
| | - Andrew P Capaldi
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
- The Bio5 Institute, University of Arizona, Tucson, AZ 85721
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Prelog M, Jeske SD, Asam C, Fuchs A, Wieser A, Gall C, Wytopil M, Mueller-Schmucker SM, Beileke S, Goekkaya M, Kling E, Geldmacher C, Rubio-Acero R, Plank M, Christa C, Willmann A, Vu M, Einhauser S, Weps M, Lampl BMJ, Almanzar G, Kousha K, Schwägerl V, Liebl B, Weber B, Drescher J, Scheidt J, Gefeller O, Messmann H, Protzer U, Liese J, Hoelscher M, Wagner R, Überla K, Steininger P. Clinical and immunological benefits of full primary COVID-19 vaccination in individuals with SARS-CoV-2 breakthrough infections: A prospective cohort study in non-hospitalized adults. J Clin Virol 2024; 170:105622. [PMID: 38091664 DOI: 10.1016/j.jcv.2023.105622] [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: 07/19/2023] [Revised: 11/23/2023] [Accepted: 11/26/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND SARS-CoV-2 variants of concern (VOC) may result in breakthrough infections (BTIs) in vaccinated individuals. The aim of this study was to investigate the effects of full primary (two-dose) COVID-19 vaccination with wild-type-based SARS-CoV-2 vaccines on symptoms and immunogenicity of SARS-CoV-2 VOC BTIs. METHODS In a longitudinal multicenter controlled cohort study in Bavaria, Germany, COVID-19 vaccinated and unvaccinated non-hospitalized individuals were prospectively enrolled within 14 days of a PCR-confirmed SARS-CoV-2 infection. Individuals were visited weekly up to 4 times, performing a structured record of medical data and viral load assessment. SARS-CoV-2-specific antibody response was characterized by anti-spike-(S)- and anti-nucleocapsid-(N)-antibody concentrations, anti-S-IgG avidity and neutralization capacity. RESULTS A total of 300 individuals (212 BTIs, 88 non-BTIs) were included with VOC Alpha or Delta SARS-CoV-2 infections. Full primary COVID-19 vaccination provided a significant effectiveness against five symptoms (relative risk reduction): fever (33 %), cough (21 %), dysgeusia (22 %), dizziness (52 %) and nausea/vomiting (48 %). Full primary vaccinated individuals showed significantly higher 50 % inhibitory concentration (IC50) values against the infecting VOC compared to unvaccinated individuals at week 1 (269 vs. 56, respectively), and weeks 5-7 (1,917 vs. 932, respectively) with significantly higher relative anti-S-IgG avidity (78% vs. 27 % at week 4, respectively). CONCLUSIONS Full primary COVID-19 vaccination reduced symptom frequencies in non-hospitalized individuals with BTIs and elicited a more rapid and longer lasting neutralization capacity against the infecting VOC compared to unvaccinated individuals. These results support the recommendation to offer at least full primary vaccination to all adults to reduce disease severity caused by immune escape-variants.
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Affiliation(s)
- Martina Prelog
- Pediatric Rheumatology / Special Immunology, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Samuel D Jeske
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Claudia Asam
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Andre Fuchs
- Internal Medicine III - Gastroenterology and Infectious Diseases, University Hospital of Augsburg, Augsburg, Germany
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Christine Gall
- Department of Medical Informatics, Biometry and Epidemiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Monika Wytopil
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sandra M Mueller-Schmucker
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Stephanie Beileke
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Mehmet Goekkaya
- Environmental Medicine, Faculty of Medicine, University of Augsburg, Institute of Environmental Medicine Helmholtz Zentrum München, German Research Center for Environmental Health, Augsburg, Germany
| | - Elisabeth Kling
- Institute of Laboratory Medicine and Microbiology University Hospital Augsburg, Augsburg, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Raquel Rubio-Acero
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Michael Plank
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | - Catharina Christa
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Annika Willmann
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Martin Vu
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Sebastian Einhauser
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Manuela Weps
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Benedikt M J Lampl
- Regensburg Department of Public Health, Division of Infection Control and Prevention, Regensburg, Germany; Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Giovanni Almanzar
- Pediatric Rheumatology / Special Immunology, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Kimia Kousha
- Pediatric Rheumatology / Special Immunology, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Valeria Schwägerl
- Pediatric Infectious Diseases, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Bernhard Liebl
- Bavarian Health and Food Safety Authority (LGL), Oberschleißheim, Germany
| | - Beatrix Weber
- Institute for Information Systems, University of Applied Sciences Hof, Hof, Germany
| | | | - Jörg Scheidt
- Institute for Information Systems, University of Applied Sciences Hof, Hof, Germany
| | - Olaf Gefeller
- Department of Medical Informatics, Biometry and Epidemiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Helmut Messmann
- Internal Medicine III - Gastroenterology and Infectious Diseases, University Hospital of Augsburg, Augsburg, Germany
| | - Ulrike Protzer
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany; Institute of Virology, Helmholtz Munich, Munich, Germany, and German Center for Infection Research, Munich partner site
| | - Johannes Liese
- Pediatric Infectious Diseases, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Ralf Wagner
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany; Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Klaus Überla
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Philipp Steininger
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
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Reinkemeyer C, Khazaei Y, Weigert M, Hannes M, Le Gleut R, Plank M, Winter S, Noreña I, Meier T, Xu L, Rubio-Acero R, Wiegrebe S, Le Thi TG, Fuchs C, Radon K, Paunovic I, Janke C, Wieser A, Küchenhoff H, Hoelscher M, Castelletti N. The Prospective COVID-19 Post-Immunization Serological Cohort in Munich (KoCo-Impf): Risk Factors and Determinants of Immune Response in Healthcare Workers. Viruses 2023; 15:1574. [PMID: 37515259 PMCID: PMC10383736 DOI: 10.3390/v15071574] [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: 06/14/2023] [Revised: 07/11/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
Antibody studies analyze immune responses to SARS-CoV-2 vaccination and infection, which is crucial for selecting vaccination strategies. In the KoCo-Impf study, conducted between 16 June and 16 December 2021, 6088 participants aged 18 and above from Munich were recruited to monitor antibodies, particularly in healthcare workers (HCWs) at higher risk of infection. Roche Elecsys® Anti-SARS-CoV-2 assays on dried blood spots were used to detect prior infections (anti-Nucleocapsid antibodies) and to indicate combinations of vaccinations/infections (anti-Spike antibodies). The anti-Spike seroprevalence was 94.7%, whereas, for anti-Nucleocapsid, it was only 6.9%. HCW status and contact with SARS-CoV-2-positive individuals were identified as infection risk factors, while vaccination and current smoking were associated with reduced risk. Older age correlated with higher anti-Nucleocapsid antibody levels, while vaccination and current smoking decreased the response. Vaccination alone or combined with infection led to higher anti-Spike antibody levels. Increasing time since the second vaccination, advancing age, and current smoking reduced the anti-Spike response. The cumulative number of cases in Munich affected the anti-Spike response over time but had no impact on anti-Nucleocapsid antibody development/seropositivity. Due to the significantly higher infection risk faced by HCWs and the limited number of significant risk factors, it is suggested that all HCWs require protection regardless of individual traits.
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Affiliation(s)
- Christina Reinkemeyer
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, 80802 Munich, Germany
| | - Yeganeh Khazaei
- Statistical Consulting Unit StaBLab, Department of Statistics, LMU Munich, Ludwigstraße 33, 80539 Munich, Germany
| | - Maximilian Weigert
- Statistical Consulting Unit StaBLab, Department of Statistics, LMU Munich, Ludwigstraße 33, 80539 Munich, Germany
- Munich Center for Machine Learning (MCML), 80539 Munich, Germany
| | - Marlene Hannes
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, 80802 Munich, Germany
| | - Ronan Le Gleut
- Institute of Computational Biology, Helmholtz Munich, 85764 Neuherberg, Germany
- Core Facility Statistical Consulting, Helmholtz Munich, 85764 Neuherberg, Germany
| | - Michael Plank
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, 80802 Munich, Germany
| | - Simon Winter
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, 80802 Munich, Germany
| | - Ivan Noreña
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, 80802 Munich, Germany
| | - Theresa Meier
- Statistical Consulting Unit StaBLab, Department of Statistics, LMU Munich, Ludwigstraße 33, 80539 Munich, Germany
| | - Lisa Xu
- Statistical Consulting Unit StaBLab, Department of Statistics, LMU Munich, Ludwigstraße 33, 80539 Munich, Germany
| | - Raquel Rubio-Acero
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, 80802 Munich, Germany
| | - Simon Wiegrebe
- Statistical Consulting Unit StaBLab, Department of Statistics, LMU Munich, Ludwigstraße 33, 80539 Munich, Germany
- Department of Genetic Epidemiology, University of Regensburg, 93053 Regensburg, Germany
| | - Thu Giang Le Thi
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Lindwurmstrasse 4, 80337 Munich, Germany
| | - Christiane Fuchs
- Institute of Computational Biology, Helmholtz Munich, 85764 Neuherberg, Germany
- Core Facility Statistical Consulting, Helmholtz Munich, 85764 Neuherberg, Germany
- Faculty of Business Administration and Economics, Bielefeld University, 33615 Bielefeld, Germany
- Center for Mathematics, Technische Universität München, 85748 Garching, Germany
| | - Katja Radon
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, 80336 Munich, Germany
- Center for International Health (CIH), University Hospital, LMU Munich, 80336 Munich, Germany
- Comprehensive Pneumology Center (CPC) Munich, German Center for Lung Research (DZL), 89337 Munich, Germany
| | - Ivana Paunovic
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, 80802 Munich, Germany
| | - Christian Janke
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, 80802 Munich, Germany
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, 80802 Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 80802 Munich, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, 80799 Munich, Germany
- Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, 80336 Munich, Germany
| | - Helmut Küchenhoff
- Statistical Consulting Unit StaBLab, Department of Statistics, LMU Munich, Ludwigstraße 33, 80539 Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, 80802 Munich, Germany
- Center for International Health (CIH), University Hospital, LMU Munich, 80336 Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 80802 Munich, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, 80799 Munich, Germany
| | - Noemi Castelletti
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, 80802 Munich, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, 80799 Munich, Germany
- Institute of Radiation Medicine, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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5
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Le Gleut R, Plank M, Pütz P, Radon K, Bakuli A, Rubio-Acero R, Paunovic I, Rieß F, Winter S, Reinkemeyer C, Schälte Y, Olbrich L, Hannes M, Kroidl I, Noreña I, Janke C, Wieser A, Hoelscher M, Fuchs C, Castelletti N. The representative COVID-19 cohort Munich (KoCo19): from the beginning of the pandemic to the Delta virus variant. BMC Infect Dis 2023; 23:466. [PMID: 37442952 DOI: 10.1186/s12879-023-08435-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Population-based serological studies allow to estimate prevalence of SARS-CoV-2 infections despite a substantial number of mild or asymptomatic disease courses. This became even more relevant for decision making after vaccination started. The KoCo19 cohort tracks the pandemic progress in the Munich general population for over two years, setting it apart in Europe. METHODS Recruitment occurred during the initial pandemic wave, including 5313 participants above 13 years from private households in Munich. Four follow-ups were held at crucial times of the pandemic, with response rates of at least 70%. Participants filled questionnaires on socio-demographics and potential risk factors of infection. From Follow-up 2, information on SARS-CoV-2 vaccination was added. SARS-CoV-2 antibody status was measured using the Roche Elecsys® Anti-SARS-CoV-2 anti-N assay (indicating previous infection) and the Roche Elecsys® Anti-SARS-CoV-2 anti-S assay (indicating previous infection and/or vaccination). This allowed us to distinguish between sources of acquired antibodies. RESULTS The SARS-CoV-2 estimated cumulative sero-prevalence increased from 1.6% (1.1-2.1%) in May 2020 to 14.5% (12.7-16.2%) in November 2021. Underreporting with respect to official numbers fluctuated with testing policies and capacities, becoming a factor of more than two during the second half of 2021. Simultaneously, the vaccination campaign against the SARS-CoV-2 virus increased the percentage of the Munich population having antibodies, with 86.8% (85.5-87.9%) having developed anti-S and/or anti-N in November 2021. Incidence rates for infections after (BTI) and without previous vaccination (INS) differed (ratio INS/BTI of 2.1, 0.7-3.6). However, the prevalence of infections was higher in the non-vaccinated population than in the vaccinated one. Considering the whole follow-up time, being born outside Germany, working in a high-risk job and living area per inhabitant were identified as risk factors for infection, while other socio-demographic and health-related variables were not. Although we obtained significant within-household clustering of SARS-CoV-2 cases, no further geospatial clustering was found. CONCLUSIONS Vaccination increased the coverage of the Munich population presenting SARS-CoV-2 antibodies, but breakthrough infections contribute to community spread. As underreporting stays relevant over time, infections can go undetected, so non-pharmaceutical measures are crucial, particularly for highly contagious strains like Omicron.
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Affiliation(s)
- Ronan Le Gleut
- Institute of Computational Biology, Helmholtz Munich, German Research Centre for Environmental Health, 85764, Neuherberg, Germany
- Core Facility Statistical Consulting, Helmholtz Munich, German Research Centre for Environmental Health, 85764, Neuherberg, Germany
| | - Michael Plank
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Peter Pütz
- Robert Koch Institute, Nordufer 20, 13353, Berlin, Germany
| | - Katja Radon
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, 80336, Munich, Germany
- Centre for International Health (CIH), University Hospital, LMU Munich, 80336, Munich, Germany
- Comprehensive Pneumology Centre (CPC) Munich, German Centre for Lung Research (DZL), 89337, Munich, Germany
| | - Abhishek Bakuli
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Raquel Rubio-Acero
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Ivana Paunovic
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Friedrich Rieß
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Simon Winter
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Christina Reinkemeyer
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Yannik Schälte
- Institute of Computational Biology, Helmholtz Munich, German Research Centre for Environmental Health, 85764, Neuherberg, Germany
- Centre for Mathematics, Technische Universität München, 85748, Garching, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Laura Olbrich
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Marlene Hannes
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Inge Kroidl
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Ivan Noreña
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Christian Janke
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
- German Centre for Infection Research (DZIF), Partner Site, Munich, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, 80799, Munich, Germany
- Max Von Pettenkofer Institute, Faculty of Medicine, LMU Munich, 80336, Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany
- Centre for International Health (CIH), University Hospital, LMU Munich, 80336, Munich, Germany
- German Centre for Infection Research (DZIF), Partner Site, Munich, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, 80799, Munich, Germany
| | - Christiane Fuchs
- Institute of Computational Biology, Helmholtz Munich, German Research Centre for Environmental Health, 85764, Neuherberg, Germany
- Core Facility Statistical Consulting, Helmholtz Munich, German Research Centre for Environmental Health, 85764, Neuherberg, Germany
- Centre for Mathematics, Technische Universität München, 85748, Garching, Germany
- Faculty of Business Administration and Economics, Bielefeld University, 33615, Bielefeld, Germany
| | - Noemi Castelletti
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802, Munich, Germany.
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, 80799, Munich, Germany.
- Institute of Radiation Medicine, Helmholtz Munich, German Research Centre for Environmental Health, 85764, Neuherberg, Germany.
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6
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Ahmed MIM, Plank M, Castelletti N, Diepers P, Eser TM, Rubio-Acero R, Noreña I, Reinkemeyer C, Zapf D, Hoelscher M, Janke C, Wieser A, Geldmacher C. Impact of Omicron Variant Infection on Assessment of Spike-Specific Immune Responses Using the EUROIMMUN Quan-T-Cell SARS-CoV-2 Assay and Roche Elecsys Anti-SARS-CoV-2-S. Diagnostics (Basel) 2023; 13:diagnostics13061024. [PMID: 36980332 PMCID: PMC10047097 DOI: 10.3390/diagnostics13061024] [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: 01/28/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
The currently prevailing variants of SARS-CoV-2 are subvariants of the Omicron variant. The aim of this study was to analyze the effect of mutations in the Spike protein of Omicron on the results Quan-T-Cell SARS-CoV-2 assays and Roche Elecsys anti-SARS-CoV-2 anti-S1. Omicron infected subjects ((n = 37), vaccinated (n = 20) and unvaccinated (n = 17)) were recruited approximately 3 weeks after a positive PCR test. The Quan-T-Cell SARS-CoV-2 assays (EUROIMMUN) using Wuhan and the Omicron adapted antigen assay and a serological test (Roche Elecsys anti-SARS-CoV-2 anti-S1) were performed. Using the original Wuhan SARS-CoV-2 IGRA TUBE, in 19 of 21 tested Omicron infected subjects, a positive IFNy response was detected, while 2 non-vaccinated but infected subjects did not respond. The Omicron adapted antigen tube resulted in comparable results. In contrast, the serological assay detected a factor 100-fold lower median Spike-specific RBD antibody concentration in non-vaccinated Omicron infected patients (n = 12) compared to patients from the pre Omicron era (n = 12) at matched time points, and eight individuals remained below the detection threshold for positivity. For vaccinated subjects, the Roche assay detected antibodies in all subjects and showed a 400 times higher median specific antibody concentration compared to non-vaccinated infected subjects in the pre-Omicron era. Our results suggest that Omicron antigen adapted IGRA stimulator tubes did not improve detection of SARS-CoV-2-specific T-cell responses in the Quant-T-Cell-SARS-CoV-2 assay. In non-vaccinated Omicron infected individuals, the Wuhan based Elecsys anti-SARS-CoV-2 anti-S1 serological assay results in many negative results at 3 weeks after diagnosis.
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Affiliation(s)
- Mohamed I M Ahmed
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81675 Munich, Germany
| | - Michael Plank
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany
| | - Noemi Castelletti
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, 80799 Munich, Germany
- Institute of Radiation Medicine, Helmholtz Munich, German Research Centre for Environmental Health, 85764 Neuherberg, Germany
| | - Paulina Diepers
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany
| | - Tabea M Eser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81675 Munich, Germany
| | - Raquel Rubio-Acero
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany
| | - Ivan Noreña
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany
| | - Christina Reinkemeyer
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany
| | - Dorinja Zapf
- Institute for Experimental Immunology, Affiliated to EUROIMMUN Medizinische Labordiagnostika AG, 23560 Lübeck, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81675 Munich, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, 80799 Munich, Germany
| | - Christian Janke
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81675 Munich, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, 80799 Munich, Germany
- Max Von Pettenkofer Institute, Faculty of Medicine, LMU Munich, 80336 Munich, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81675 Munich, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology, Infection and Pandemic Research, 80799 Munich, Germany
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7
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Ahmed MIM, Diepers P, Janke C, Plank M, Eser TM, Rubio-Acero R, Fuchs A, Baranov O, Castelletti N, Kroidl I, Olbrich L, Bauer B, Wang D, Prelog M, Liese JG, Reinkemeyer C, Hoelscher M, Steininger P, Überla K, Wieser A, Geldmacher C. Enhanced Spike-specific, but attenuated Nucleocapsid-specific T cell responses upon SARS-CoV-2 breakthrough versus non-breakthrough infections. Front Immunol 2022; 13:1026473. [PMID: 36582222 PMCID: PMC9792977 DOI: 10.3389/fimmu.2022.1026473] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 08/23/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 vaccine breakthrough infections frequently occurred even before the emergence of Omicron variants. Yet, relatively little is known about the impact of vaccination on SARS-CoV-2-specific T cell and antibody response dynamics upon breakthrough infection. We have therefore studied the dynamics of CD4 and CD8 T cells targeting the vaccine-encoded Spike and the non-encoded Nucleocapsid antigens during breakthrough infections (BTI, n=24) and in unvaccinated control infections (non-BTI, n=30). Subjects with vaccine breakthrough infection had significantly higher CD4 and CD8 T cell responses targeting the vaccine-encoded Spike during the first and third/fourth week after PCR diagnosis compared to non-vaccinated controls, respectively. In contrast, CD4 T cells targeting the non-vaccine encoded Nucleocapsid antigen were of significantly lower magnitude in BTI as compared to non-BTI. Hence, previous vaccination was linked to enhanced T cell responses targeting the vaccine-encoded Spike antigen, while responses against the non-vaccine encoded Nucleocapsid antigen were significantly attenuated.
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Affiliation(s)
- Mohamed Ibraheem Mahmoud Ahmed
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany,German Centre for Infection Research (DZIF), Munich, Germany
| | - Paulina Diepers
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Christian Janke
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Michael Plank
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Tabea M. Eser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany,German Centre for Infection Research (DZIF), Munich, Germany
| | - Raquel Rubio-Acero
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Anna Fuchs
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Olga Baranov
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany,German Centre for Infection Research (DZIF), Munich, Germany
| | - Noemi Castelletti
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Inge Kroidl
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany,German Centre for Infection Research (DZIF), Munich, Germany
| | - Laura Olbrich
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany,German Centre for Infection Research (DZIF), Munich, Germany,Oxford Vaccine Group, Department of Paediatrics, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Bernadette Bauer
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Danni Wang
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Martina Prelog
- Pediatric Rheumatology/Special Immunology, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Johannes G. Liese
- Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Christina Reinkemeyer
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany,German Centre for Infection Research (DZIF), Munich, Germany
| | - Philipp Steininger
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Klaus Überla
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany,German Centre for Infection Research (DZIF), Munich, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany,German Centre for Infection Research (DZIF), Munich, Germany,*Correspondence: Christof Geldmacher,
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8
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Liu W, Patouret R, Barluenga S, Plank M, Loewith R, Winssinger N. Identification of a Covalent Importin-5 Inhibitor, Goyazensolide, from a Collective Synthesis of Furanoheliangolides. ACS Cent Sci 2021; 7:954-962. [PMID: 34235256 PMCID: PMC8227592 DOI: 10.1021/acscentsci.1c00056] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Indexed: 06/13/2023]
Abstract
Sesquiterpenes are a rich source of covalent inhibitors with a long history in traditional medicine and include several important therapeutics and tool compounds. Herein, we report the total synthesis of 16 sesquiterpene lactones via a build/couple/pair strategy, including goyasensolide. Using an alkyne-tagged cellular probe and proteomics analysis, we discovered that goyazensolide selectively targets the oncoprotein importin-5 (IPO5) for covalent engagement. We further demonstrate that goyazensolide inhibits the translocation of RASAL-2, a cargo of IPO5, into the nucleus and perturbs the binding between IPO5 and two specific viral nuclear localization sequences.
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Affiliation(s)
- Weilong Liu
- Department
of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Rémi Patouret
- Department
of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Sofia Barluenga
- Department
of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Michael Plank
- Department
of Molecular Biology, NCCR Chemical Biology, Faculty of Science, University of Geneva, 1205 Geneva, Switzerland
| | - Robbie Loewith
- Department
of Molecular Biology, NCCR Chemical Biology, Faculty of Science, University of Geneva, 1205 Geneva, Switzerland
| | - Nicolas Winssinger
- Department
of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva, Switzerland
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9
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Plank M, Berti M, Loewith R. Phosphoproteomic Effects of Acute Depletion of PP2A Regulatory Subunit Cdc55. Proteomics 2020; 21:e2000166. [PMID: 32970932 DOI: 10.1002/pmic.202000166] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/15/2020] [Indexed: 11/08/2022]
Abstract
Protein phosphatase regulatory subunits are increasingly recognized as promising drug targets. In the absence of an existing drug, inducible degradation provides a means of predicting candidate targets. Here auxin-inducible degradation of Saccharomyces cerevisiae PP2A regulatory subunit Cdc55 in combination with quantitative phosphoproteomics is employed. A prevalence of hyperphosphorylated phosphopeptides indicates that the approach successfully identified direct PP2ACdc55 targets. PRM follow up of data-dependent acquisition results confirmed that vacuolar amino acid transporters are among the proteins most strongly affected by Cdc55 depletion.
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Affiliation(s)
- Michael Plank
- Department of Molecular Biology, University of Geneva, Geneva, CH-1211, Switzerland.,National Centre of Competence in Research-Chemical Biology, University of Geneva, Geneva, CH-1211, Switzerland
| | - Marina Berti
- Department of Molecular Biology, University of Geneva, Geneva, CH-1211, Switzerland
| | - Robbie Loewith
- Department of Molecular Biology, University of Geneva, Geneva, CH-1211, Switzerland.,National Centre of Competence in Research-Chemical Biology, University of Geneva, Geneva, CH-1211, Switzerland
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10
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Plank M, Perepelkina M, Müller M, Vaga S, Zou X, Bourgoint C, Berti M, Saarbach J, Haesendonckx S, Winssinger N, Aebersold R, Loewith R. Chemical Genetics of AGC-kinases Reveals Shared Targets of Ypk1, Protein Kinase A and Sch9. Mol Cell Proteomics 2020; 19:655-671. [PMID: 32102971 PMCID: PMC7124472 DOI: 10.1074/mcp.ra120.001955] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Indexed: 12/22/2022] Open
Abstract
Protein phosphorylation cascades play a central role in the regulation of cell growth and protein kinases PKA, Sch9 and Ypk1 take center stage in regulating this process in S. cerevisiae To understand how these kinases co-ordinately regulate cellular functions we compared the phospho-proteome of exponentially growing cells without and with acute chemical inhibition of PKA, Sch9 and Ypk1. Sites hypo-phosphorylated upon PKA and Sch9 inhibition were preferentially located in RRxS/T-motifs suggesting that many are directly phosphorylated by these enzymes. Interestingly, when inhibiting Ypk1 we not only detected several hypo-phosphorylated sites in the previously reported RxRxxS/T-, but also in an RRxS/T-motif. Validation experiments revealed that neutral trehalase Nth1, a known PKA target, is additionally phosphorylated and activated downstream of Ypk1. Signaling through Ypk1 is therefore more closely related to PKA- and Sch9-signaling than previously appreciated and may perform functions previously only attributed to the latter kinases.
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Affiliation(s)
- Michael Plank
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland; National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland.
| | - Mariya Perepelkina
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Markus Müller
- National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland; Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Stefania Vaga
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Xiaoming Zou
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Clélia Bourgoint
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Marina Berti
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Jacques Saarbach
- National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, CH-1211, Geneva, Switzerland
| | - Steven Haesendonckx
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland
| | - Nicolas Winssinger
- National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland; Department of Organic Chemistry, University of Geneva, CH-1211, Geneva, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, CH-8093 Zürich, Switzerland; Faculty of Science, University of Zurich, CH-8006, Zurich, Switzerland
| | - Robbie Loewith
- Department of Molecular Biology, University of Geneva, CH-1211, Geneva, Switzerland; National Centre of Competence in Research - Chemical Biology, University of Geneva, CH-1211, Geneva, Switzerland.
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11
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Marks E, Naudin C, Nolan G, Goggins BJ, Burns G, Mateer SW, Latimore JK, Minahan K, Plank M, Foster PS, Callister R, Veysey M, Walker MM, Talley NJ, Radford-Smith G, Keely S. Regulation of IL-12p40 by HIF controls Th1/Th17 responses to prevent mucosal inflammation. Mucosal Immunol 2017; 10:1224-1236. [PMID: 28120851 DOI: 10.1038/mi.2016.135] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 12/06/2016] [Indexed: 02/04/2023]
Abstract
Intestinal inflammatory lesions are inherently hypoxic, due to increased metabolic demands created by cellular infiltration and proliferation, and reduced oxygen supply due to vascular damage. Hypoxia stabilizes the transcription factor hypoxia-inducible factor-1α (HIF) leading to a coordinated induction of endogenously protective pathways. We identified IL12B as a HIF-regulated gene and aimed to define how the HIF-IL-12p40 axis influenced intestinal inflammation. Intestinal lamina propria lymphocytes (LPL) were characterized in wild-type and IL-12p40-/- murine colitis treated with vehicle or HIF-stabilizing prolyl-hydroxylase inhibitors (PHDi). IL12B promoter analysis was performed to examine hypoxia-responsive elements. Immunoblot analysis of murine and human LPL supernatants was performed to characterize the HIF/IL-12p40 signaling axis. We observed selective induction of IL-12p40 following PHDi-treatment, concurrent with suppression of Th1 and Th17 responses in murine colitis models. In the absence of IL-12p40, PHDi-treatment was ineffective. Analysis of the IL12B promoter identified canonical HIF-binding sites. HIF stabilization in LPLs resulted in production of IL-12p40 homodimer which was protective against colitis. The selective induction of IL-12p40 by HIF-1α leads to a suppression of mucosal Th1 and Th17 responses. This HIF-IL12p40 axis may represent an endogenously protective mechanism to limit the progression of chronic inflammation, shifting from pro-inflammatory IL-12p70 to an antagonistic IL-12p40 homodimer.
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Affiliation(s)
- E Marks
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - C Naudin
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - G Nolan
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - B J Goggins
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia.,Priority Research Centre for Digestive Health and Neurogastroenterology, University of Newcastle, Newcastle, New South Wales, Australia
| | - G Burns
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia.,Priority Research Centre for Digestive Health and Neurogastroenterology, University of Newcastle, Newcastle, New South Wales, Australia
| | - S W Mateer
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia.,Priority Research Centre for Digestive Health and Neurogastroenterology, University of Newcastle, Newcastle, New South Wales, Australia
| | - J K Latimore
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia.,Priority Research Centre for Digestive Health and Neurogastroenterology, University of Newcastle, Newcastle, New South Wales, Australia
| | - K Minahan
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia.,Priority Research Centre for Digestive Health and Neurogastroenterology, University of Newcastle, Newcastle, New South Wales, Australia
| | - M Plank
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - P S Foster
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - R Callister
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.,Priority Research Centre for Digestive Health and Neurogastroenterology, University of Newcastle, Newcastle, New South Wales, Australia
| | - M Veysey
- Priority Research Centre for Digestive Health and Neurogastroenterology, University of Newcastle, Newcastle, New South Wales, Australia.,School of Medicine, Public Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - M M Walker
- Priority Research Centre for Digestive Health and Neurogastroenterology, University of Newcastle, Newcastle, New South Wales, Australia.,School of Medicine, Public Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - N J Talley
- Priority Research Centre for Digestive Health and Neurogastroenterology, University of Newcastle, Newcastle, New South Wales, Australia.,School of Medicine, Public Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - G Radford-Smith
- Royal Brisbane and Women's Hospital, Brisbane, School of Medicine, University of Queensland, Brisbane, Queensland, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - S Keely
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia.,Priority Research Centre for Digestive Health and Neurogastroenterology, University of Newcastle, Newcastle, New South Wales, Australia
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12
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Plank M, Fischer R, Geoghegan V, Charles PD, Konietzny R, Acuto O, Pears C, Schofield CJ, Kessler BM. Expanding the yeast protein arginine methylome. Proteomics 2015; 15:3232-43. [DOI: 10.1002/pmic.201500032] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/27/2015] [Accepted: 06/02/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Michael Plank
- Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Oxford UK
- Chemistry Research Laboratory; University of Oxford; Oxford UK
| | - Roman Fischer
- Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Oxford UK
| | - Vincent Geoghegan
- Sir William Dunn School of Pathology; University of Oxford; Oxford UK
| | - Philip D. Charles
- Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Oxford UK
| | - Rebecca Konietzny
- Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Oxford UK
| | - Oreste Acuto
- Sir William Dunn School of Pathology; University of Oxford; Oxford UK
| | | | | | - Benedikt M. Kessler
- Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Oxford UK
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13
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Corradini E, Burgers PP, Plank M, Heck AJR, Scholten A. Huntingtin-associated protein 1 (HAP1) is a cGMP-dependent kinase anchoring protein (GKAP) specific for the cGMP-dependent protein kinase Iβ isoform. J Biol Chem 2015; 290:7887-96. [PMID: 25653285 DOI: 10.1074/jbc.m114.622613] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Protein-protein interactions are important in providing compartmentalization and specificity in cellular signal transduction. Many studies have hallmarked the well designed compartmentalization of the cAMP-dependent protein kinase (PKA) through its anchoring proteins. Much less data are available on the compartmentalization of its closest homolog, cGMP-dependent protein kinase (PKG), via its own PKG anchoring proteins (GKAPs). For the enrichment, screening, and discovery of (novel) PKA anchoring proteins, a plethora of methodologies is available, including our previously described chemical proteomics approach based on immobilized cAMP or cGMP. Although this method was demonstrated to be effective, each immobilized cyclic nucleotide did not discriminate in the enrichment for either PKA or PKG and their secondary interactors. Hence, with PKG signaling components being less abundant in most tissues, it turned out to be challenging to enrich and identify GKAPs. Here we extend this cAMP-based chemical proteomics approach using competitive concentrations of free cyclic nucleotides to isolate each kinase and its secondary interactors. Using this approach, we identified Huntingtin-associated protein 1 (HAP1) as a putative novel GKAP. Through sequence alignment with known GKAPs and secondary structure prediction analysis, we defined a small sequence domain mediating the interaction with PKG Iβ but not PKG Iα. In vitro binding studies and site-directed mutagenesis further confirmed the specificity and affinity of HAP1 binding to the PKG Iβ N terminus. These data fully support that HAP1 is a GKAP, anchoring specifically to the cGMP-dependent protein kinase isoform Iβ, and provide further evidence that also PKG spatiotemporal signaling is largely controlled by anchoring proteins.
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Affiliation(s)
- Eleonora Corradini
- From the Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Pepijn P Burgers
- From the Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Michael Plank
- From the Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- From the Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Arjen Scholten
- From the Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Plank M, Maltby S, Mattes J, Foster PS. Targeting translational control as a novel way to treat inflammatory disease: the emerging role of microRNAs. Clin Exp Allergy 2014; 43:981-99. [PMID: 23957346 DOI: 10.1111/cea.12170] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Chronic inflammatory diseases (e.g. asthma and chronic obstructive pulmonary disease)are leading causes of morbidity and mortality world-wide and effective treatments are limited. These disorders can often be attributed to abnormal immune responses to environmental stimuli and infections. Mechanisms leading to inflammation are complex,resulting from interactions of structural cells and activation of both the adaptive and innate arms of the immune system. The activation of structural and immune cells involves both temporary and permanent changes in gene expression in these cells, which underpin chronic inflammation and tissue dysfunction. miRNAs are small non-coding RNAs increasingly being recognized to play important roles in the post-transcriptional regulation of gene expression in mammalian cells by regulating translation. Individual miRNA scan exert their effects by directly inhibiting the translation or stability of multiple mRNAs simultaneously. Thus, the expression or blockade of function of a single miRNA (miR) can result in pronounced alterations in protein expression within a given cell. Dysregulation of miRNA expression may subsequently alter cellular function, and in certain situations predispose to disease. Our current understanding of the role of miRNA in the regulation of inflammatory disease (e.g. allergic diseases) remains limited. In this review, we provide an overview of the current understanding of miRNA biogenesis and function, the roles miRNA play in the regulation of immune cell function and their potential contribution to inflammatory diseases. We also highlight strategies to alter miRNA function for experimental or therapeutic gain, and discuss the potential utility and limitations of targeting these molecules as anti-inflammatory strategies.
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Affiliation(s)
- M Plank
- Priority Research Centre for Asthma and Respiratory Disease, Department of Microbiology and Immunology, School of Pharmacy and Biomedical Sciences, Faculty of Health and Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
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15
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Plank M, Maltby S, Mattes J, Foster PS. Targeting translational control as a novel way to treat inflammatory disease: the emerging role of MicroRNAs. Clin Exp Allergy 2013. [DOI: 10.1111/cea.12135] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- M. Plank
- Priority Research Centre for Asthma and Respiratory Disease; Department of Microbiology and Immunology; School of Pharmacy and Biomedical Sciences; Faculty of Health and Hunter Medical Research Institute; University of Newcastle; Newcastle; NSW; Australia
| | - S. Maltby
- Priority Research Centre for Asthma and Respiratory Disease; Department of Microbiology and Immunology; School of Pharmacy and Biomedical Sciences; Faculty of Health and Hunter Medical Research Institute; University of Newcastle; Newcastle; NSW; Australia
| | | | - P. S. Foster
- Priority Research Centre for Asthma and Respiratory Disease; Department of Microbiology and Immunology; School of Pharmacy and Biomedical Sciences; Faculty of Health and Hunter Medical Research Institute; University of Newcastle; Newcastle; NSW; Australia
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Corradini E, Burgers PP, Plank M, Heck AJR, Scholten A. A tissue based chemical proteomics screen to identify novel G-kinase associated proteins (GKAPs). BMC Pharmacol Toxicol 2013. [PMCID: PMC3765688 DOI: 10.1186/2050-6511-14-s1-p16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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17
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Hlawatsch J, Karlstetter M, Aslanidis A, Lückoff A, Walczak Y, Plank M, Böck J, Langmann T. Sterile alpha motif containing 7 (samd7) is a novel crx-regulated transcriptional repressor in the retina. PLoS One 2013; 8:e60633. [PMID: 23565263 PMCID: PMC3615016 DOI: 10.1371/journal.pone.0060633] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 03/01/2013] [Indexed: 11/18/2022] Open
Abstract
Inherited retinal diseases are mainly caused by mutations in genes that are highly expressed in photoreceptors of the retina. The majority of these genes is under the control of the transcription factor Cone rod homeobox (Crx), that acts as a master transcription factor in photoreceptors. Using a genome-wide chromatin immunoprecipitation dataset that highlights all potential in vivo targets of Crx, we have identified a novel sterile alpha motif (SAM) domain containing protein, Samd7. mRNA Expression of Samd7 was confined to the late postnatal and adult mouse retina as well as the pineal gland. Using immunohistochemistry and Western blot, we could detect Samd7 protein in the outer nuclear layer of adult mouse retina. Ectopic over-expression in HEK293 cells demonstrated that Samd7 resides in the cytoplasm as well as the nucleus. In vitro electroporation of fluorescent reporters into living mouse retinal cultures revealed that transcription of the Samd7 gene depends on evolutionary conserved Crx motifs located in the first intron enhancer. Moreover, Crx knock-down with shRNA strongly reduced Samd7 reporter activity and endogenous Samd7 protein, indicating that Crx is required for retinal expression of Samd7. Finally, using co-transfections in luciferase reporter assays we found that Samd7 interferes with Crx-dependent transcription. Samd7 suppressed luciferase activity from a reporter plasmid with five Crx consensus repeats in a dose dependent manner and reduced Crx-mediated transactivation of regulatory sequences in the retinoschisin gene and the Samd7 gene itself. Taken together, we have identified a novel retinal SAM domain protein, Samd7, which could act as a transcriptional repressor involved in fine-tuning of Crx-regulated gene expression.
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Affiliation(s)
- Julia Hlawatsch
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Marcus Karlstetter
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
- Department of Ophthalmology, University of Cologne, Cologne, Germany
| | - Alexander Aslanidis
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
- Department of Ophthalmology, University of Cologne, Cologne, Germany
| | - Anika Lückoff
- Department of Ophthalmology, University of Cologne, Cologne, Germany
| | - Yana Walczak
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
- Department of Ophthalmology, University of Cologne, Cologne, Germany
| | - Michael Plank
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Julia Böck
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Thomas Langmann
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
- Department of Ophthalmology, University of Cologne, Cologne, Germany
- * E-mail:
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18
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Plank M, Hu G, Silva AS, Wood SH, Hesketh EE, Janssens G, Macedo A, de Magalhães JP, Church GM. An analysis and validation pipeline for large-scale RNAi-based screens. Sci Rep 2013; 3:1076. [PMID: 23326633 PMCID: PMC3546318 DOI: 10.1038/srep01076] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 11/22/2012] [Indexed: 12/16/2022] Open
Abstract
Large-scale RNAi-based screens are a major technology, but require adequate prioritization and validation of candidate genes from the primary screen. In this work, we performed a large-scale pooled shRNA screen in mouse embryonic stem cells (ESCs) to discover genes associated with oxidative stress resistance and found several candidates. We then developed a bioinformatics pipeline to prioritize these candidates incorporating effect sizes, functional enrichment analysis, interaction networks and gene expression information. To validate candidates, we mixed normal cells with cells expressing the shRNA coupled to a fluorescent protein, which allows control cells to be used as an internal standard, and thus we could detect shRNAs with subtle effects. Although we did not identify genes associated with oxidative stress resistance, as a proof-of-concept of our pipeline we demonstrate a detrimental role of Edd1 silencing in ESC growth. Our methods may be useful for candidate gene prioritization of large-scale RNAi-based screens.
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Affiliation(s)
- Michael Plank
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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Urgen BA, Plank M, Kutas M, Poizner H, Saygin AP. Temporal Characteristics of Neural Processing During Action Perception: The Role of Biological Form and Biological Motion. J Vis 2012. [DOI: 10.1167/12.9.643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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21
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Plank M, Wuttke D, van Dam S, Clarke SA, de Magalhães JP. A meta-analysis of caloric restriction gene expression profiles to infer common signatures and regulatory mechanisms. Mol Biosyst 2012; 8:1339-49. [PMID: 22327899 DOI: 10.1039/c2mb05255e] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Caloric restriction, a reduction in calorie intake without malnutrition, retards age-related degeneration and extends lifespan in several organisms. CR induces multiple changes, yet its underlying mechanisms remain poorly understood. In this work, we first performed a meta-analysis of microarray CR studies in mammals and identified genes and processes robustly altered due to CR. Our results reveal a complex array of CR-induced changes and we re-identified several genes and processes previously associated with CR, such as growth hormone signalling, lipid metabolism and immune response. Moreover, our results highlight novel associations with CR, such as retinol metabolism and copper ion detoxification, as well as hint of a strong effect of CR on circadian rhythms that in turn may contribute to metabolic changes. Analyses of our signatures by integrating co-expression data, information on genetic mutants, and transcription factor binding site analysis revealed candidate regulators of transcriptional modules in CR. Our results hint at a transcriptional module involved in sterol metabolism regulated by Srebf1. A putative regulatory role of Ppara was also identified. Overall, our conserved molecular signatures of CR provide a comprehensive picture of CR-induced changes and help understand its regulatory mechanisms.
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Affiliation(s)
- Michael Plank
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
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de Magalhães JP, Wuttke D, Wood SH, Plank M, Vora C. Genome-environment interactions that modulate aging: powerful targets for drug discovery. Pharmacol Rev 2011; 64:88-101. [PMID: 22090473 DOI: 10.1124/pr.110.004499] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aging is the major biomedical challenge of this century. The percentage of elderly people, and consequently the incidence of age-related diseases such as heart disease, cancer, and neurodegenerative diseases, is projected to increase considerably in the coming decades. Findings from model organisms have revealed that aging is a surprisingly plastic process that can be manipulated by both genetic and environmental factors. Here we review a broad range of findings in model organisms, from environmental to genetic manipulations of aging, with a focus on those with underlying gene-environment interactions with potential for drug discovery and development. One well-studied dietary manipulation of aging is caloric restriction, which consists of restricting the food intake of organisms without triggering malnutrition and has been shown to retard aging in model organisms. Caloric restriction is already being used as a paradigm for developing compounds that mimic its life-extension effects and might therefore have therapeutic value. The potential for further advances in this field is immense; hundreds of genes in several pathways have recently emerged as regulators of aging and caloric restriction in model organisms. Some of these genes, such as IGF1R and FOXO3, have also been associated with human longevity in genetic association studies. The parallel emergence of network approaches offers prospects to develop multitarget drugs and combinatorial therapies. Understanding how the environment modulates aging-related genes may lead to human applications and disease therapies through diet, lifestyle, or pharmacological interventions. Unlocking the capacity to manipulate human aging would result in unprecedented health benefits.
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Affiliation(s)
- João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
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Affiliation(s)
- M. Plank
- Department of Animal Biodiversity University of Vienna Vienna Austria
- Austrian Coordination Centre for Bat Conservation and Research (KFFOE) Leonding Austria
| | - K. Fiedler
- Department of Animal Biodiversity University of Vienna Vienna Austria
| | - G. Reiter
- Austrian Coordination Centre for Bat Conservation and Research (KFFOE) Leonding Austria
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Plank M, Wadhams GH, Leake MC. Millisecond timescale slimfield imaging and automated quantification of single fluorescent protein molecules for use in probing complex biological processes. Integr Biol (Camb) 2009; 1:602-12. [PMID: 20023777 DOI: 10.1039/b907837a] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescence microscopy offers a minimally perturbative approach to probe biology in vivo. However, available techniques are limited both in sensitivity and temporal resolution for commonly used fluorescent proteins. Here we present a new imaging system with a diagnostic toolkit that caters for the detection and quantification of fluorescent proteins for use in fast functional imaging at the single-molecule level. It utilizes customized microscopy with a mode of illumination we call "slimfield" suitable for rapid (approximately millisecond) temporal resolution on a range of common fluorescent proteins. Slimfield is cheap and simple, allowing excitation intensities approximately 100 times greater than those of widefield imaging, permitting single-molecule detection at high speed. We demonstrate its application on several purified fluorescent proteins in standard use as genetically-encoded reporter molecules. Controlled in vitro experiments indicate single protein molecules over a field of view of approximately 30 microm(2) area, large enough to encapsulate complete prokaryotic and small eukaryotic cells. Using a novel diagnostic toolkit we demonstrate automated detection and quantification of single molecules with maximum imaging rates for a 128 x 128 pixel array of approximately 500 frames per second with a localization precision for these photophysically poor fluorophores to within 50 nm. We report for the first time the imaging of the dim enhanced cyan fluorescent protein (ECFP) and CyPet at the single-molecule level. Applying modifications, we performed simultaneous dual-colour slimfield imaging for use in co-localization and FRET. We present preliminary in vivo imaging on bacterial cells and demonstrate approximately millisecond timescale functional imaging at the single-molecule level with negligible photodamage.
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Affiliation(s)
- Michael Plank
- Clarendon Laboratory, Oxford Physics, Oxford University, Parks Road, Oxford, UK
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25
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Meredith DH, Plank M, Lewis PJ. Different patterns of integral membrane protein localization during cell division in Bacillus subtilis. Microbiology (Reading) 2008; 154:64-71. [PMID: 18174126 DOI: 10.1099/mic.0.2007/013268-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cell division in rod-shaped bacteria nearly always occurs exactly at mid-cell and is dependent on the formation of the cytokinetic FtsZ ring and its associated division proteins. Many thousands of copies of division, or septum-specific proteins assemble at this site and may lead to the exclusion of other integral membrane proteins that are normally able to diffuse freely throughout the cytoplasmic membrane. In this study we have investigated the localization of a series of integral membrane proteins in Bacillus subtilis and we show that the recruitment of division and septum-specific proteins does not necessarily preclude the diffusion of other integral membrane proteins. However, some proteins, namely ATP synthase and succinate dehydrogenase, are reduced/absent from the mid-cell region at the onset of cell division, which may reflect an association with lipid domains rich in phosphatidylglycerol that are thought to be present at diminished levels at sites of cell division.
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Affiliation(s)
- D H Meredith
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - M Plank
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - P J Lewis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
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James A, Dungan R, Plank M, Ito R. A dynamical model of honeydew droplet production by sooty-beech scale insects (Ultracoelostoma spp.) in New Zealand Nothofagus forest. Ecol Modell 2007. [DOI: 10.1016/j.ecolmodel.2007.06.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Comerford A, Plank M, David T. eNOS and Ca2+ production in arterial geometries: An integrated fluid mechanics/cell model. J Biomech 2006. [DOI: 10.1016/s0021-9290(06)84510-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Kiefer RT, Ploppa A, Krueger WA, Plank M, Nohé B, Haeberle HA, Unertl K, Dieterich HJ. Local anesthetics impair human granulocyte phagocytosis activity, oxidative burst, and CD11b expression in response to Staphylococcus aureus. Anesthesiology 2003; 98:842-8. [PMID: 12657844 DOI: 10.1097/00000542-200304000-00009] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND With invasion of bacteria, the host defense system is activated by a complex cascade of various mechanisms. Local anesthetics previously were shown to interact with diverse components of the immune response, such as leukocyte adherence on endothelial monolayers, oxidative burst, or crosstalk within lymphocyte subset populations. However, effects of newer local anesthetics like bupivacaine and ropivacaine on antibacterial host defense-primarily phagocytosis activity, oxidative burst, or CD11b expression-still remain unclear. METHODS Whole blood samples were preincubated with local anesthetics (lidocaine, 9.2, 92.2, and 1,846 microm bupivacaine, 6.1, 61, and 770 microm; ropivacaine, 6.4, 64, and 801 microm). For the oxidative burst and CD11b assay, dihydroethidium was added to the probes. After viable Staphylococcus aureus was added in a 5 to 1 ratio following leukocyte count, phagocytosis was stopped at different times, and staining with monoclonal antibodies was performed for subsequent flow cytometric analysis of phagocytosis activity, oxidative burst, and CD11b expression. RESULTS Granulocyte phagocytosis activity, CD11b expression, and generation of reactive oxygen species were significantly reduced by lidocaine (P < 0.0002) and bupivacaine (P < 0.005) in the highest concentration (1,846 microm and 770 microm, respectively). The capability of granulocytes to ingest bacteria was significantly depressed only by lidocaine (P < 0.003). Ropivacaine had no significant effect on any parameter investigated. CONCLUSIONS Local anesthetic dose and structure dependently inhibit inflammatory and immunologic parameters of granulocyte functions. Ropivacaine shows low interference with granulocyte immunologic and inflammatory functions.
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Affiliation(s)
- Ralph-Thomas Kiefer
- Department of Anesthesiology and Intensive Care Medicine, Eberhard-Karls University, Tuebingen, Germany.
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Geldmacher J, Plank M, Treuheit KD. [Significance of the preoperative status in the evaluation of results of the reconstruction of extensor tendons]. HANDCHIR MIKROCHIR P 1986; 18:23-9. [PMID: 3949258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Since 1977, a new evaluation scheme that is simple to use and which provides more objective information than earlier plans has been employed for the assessment of the results of extensor tendon reconstruction. The results in the four groups were evaluated and given a prognosis in accordance with the newly developed scheme. This permitted not only a better differentiation of the value of the therapeutic procedures, but also allowed one to make prognostic predictions. The prognosis is also of particular importance during preoperative talks with the patient.
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Offenkrantz W, Bing R, Buckey C, Hayes H, Kelley J, King J, Lange M, Overly K, Plank M, Rehmar J, Skillman M, Sullivan D. A psychoanalytically oriented case conference for occupational therapy students. Am J Occup Ther 1967; 21:70-5. [PMID: 6068860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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